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rebeccamycin

CHEBI:135511 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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.

An N-glycosyl compound consisting of a heteropolycyclic ring system with a glucosyl group attached to one of the indolic nitrogens.

Structure

Standard InChIKeyQEHOIJJIZXRMAN-QZQSLCQPSA-N
SMILESCO[C@@H]1[C@H](O[C@H]([C@@H]([C@H]1O)O)N2C3=C(C=CC=C3Cl)C4=C5C(=C6C7=C(C(=CC=C7)Cl)NC6=C42)C(=O)NC5=O)CO
Stereochemistryfully defined
Cross-referencesnpatlas:NPA08169, pubchem:73110

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.

TaxonBasisClusterEvidence
Lechevalieria aerocolonigenes
NCBITaxon:68170		 SOURCE_ASSERTION mibig:BGC0000821 PMID:15743957

Occurrences 6

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
Nocardia
NCBITaxon:1817		 LOTUS DOI:10.1016/S0040-4039(00)89280-1
Streptomyces lividans
NCBITaxon:1916		 LOTUS DOI:10.1038/JA.2015.31
Streptomyces sanyensis
NCBITaxon:568869		 LOTUS DOI:10.3390/MD17100588
Lechevalieria aerocolonigenes
NCBITaxon:68170		 LOTUS DOI:10.1021/NP50059A020
Lechevalieria aerocolonigenes
NCBITaxon:68170		 LOTUS DOI:10.1128/JB.187.6.2084-2092.2005
Lechevalieria aerocolonigenes
NCBITaxon:68170		 LOTUS DOI:10.7164/ANTIBIOTICS.40.668

Biosynthetic gene clusters 1

AccessionHostLocus evidenceGenome
mibig:BGC0000821 Lechevalieria aerocolonigenes
NCBITaxon:68170 		CLUSTER_DEMONSTRATED genbank:AB090952.1

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 RebG 4'-demethylrebeccamycin synthase
UniProtKB:Q8KHE4		 RHEA:27397 CHEBI:330772 + CHEBI:15903 → CHEBI:595389 DOI:10.1002/cbic.200500504
2 RebM demethylrebeccamycin-D-glucose O-methyltransferase
UniProtKB:Q8KZ94		 RHEA:27353 CHEBI:595389 + CHEBI:59789 → CHEBI:135511 DOI:10.1074/jbc.M800503200

Step 1: RebG N-glucosylates dichloroarcyriaflavin A to form 4'-demethylrebeccamycin in the penultimate rebeccamycin biosynthetic step; Rhea maps the corresponding EC 4.3.3.5 reaction to RHEA:27397.

Step 2: RebM transfers the SAM methyl group to 4'-demethylrebeccamycin in the terminal O-methylation that forms rebeccamycin; Rhea maps this EC 2.1.1.164 reaction to RHEA:27353.

Mechanism & Biosynthesis Overview

PRODUCERS & OCCURRENCE 1 producer (0 causal) 6 cited occurrences BIOSYNTHETIC LOCUS 1 gene cluster 2 curated pathway steps NATURAL PRODUCT rebeccamycin CHEBI:135511 Alkaloids TARGETS & BIOACTIVITY 0 molecular targets 0 bioactivities · 12 graphs

Causal graph — biosynthesis 3 nodes, 2 edges

Partial L. aerocolonigenes rebeccamycin biosynthesis graph for RebM-catalyzed terminal 4'-O-methylation.

SubjectPredicateObjectNotesEvidence
4'-demethylrebeccamycin is methylated by RebM demethylrebeccamycin-D-glucose O-methyltransferase RebM methylates the glucosyl 4'-hydroxy group of 4'-demethylrebeccamycin.
DOI:10.1074/jbc.M800503200
DOI:10.1002/cbic.200500504
https://mibig.secondarymetabolites.org/repository/BGC0000821.5/BGC0000821.gbk
https://www.uniprot.org/uniprotkb/Q8KZ94
https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv
  • reference
    DOI:10.1074/jbc.M800503200
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    RebM catalyzes glucosyl C-4′ O-methylation as the final step in rebeccamycin biosynthesis
    notes
    Singh et al. expressed Lechevalieria aerocolonigenes RebM from the pCST28aRebM construct, crystallized the enzyme, and analyzed SAM-dependent O-methyltransferase catalysis by the wild type enzyme and site-directed mutants.
  • reference
    DOI:10.1002/cbic.200500504
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    in vitro RebM-catalyzed 4′-O-methylation
    notes
    Zhang et al. established that rebM encodes the rebeccamycin 4'-O-methyltransferase and showed in vitro RebM methylation of RebG-derived indolocarbazole glucosides.
  • reference
    https://mibig.secondarymetabolites.org/repository/BGC0000821.5/BGC0000821.gbk
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    MIBiG BGC0000821.5 maps the L. aerocolonigenes AB090952 rebeccamycin biosynthetic gene cluster CDS BAC10678.1 to rebM.
  • reference
    https://www.uniprot.org/uniprotkb/Q8KZ94
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    Reviewed UniProtKB:Q8KZ94 is the 283 aa L. aerocolonigenes RebM demethylrebeccamycin-D-glucose O-methyltransferase, cross-references AB090952 protein BAC10678.1, and annotates RHEA:27353 from PMID:18502766.
  • reference
    https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    The Rhea Swiss-Prot mapping links UniProtKB:Q8KZ94 to the RebM O-methyltransferase reaction RHEA:27353.
RebM demethylrebeccamycin-D-glucose O-methyltransferase forms rebeccamycin The SAM-dependent RebM reaction forms the final O-methylated rebeccamycin structure.
DOI:10.1074/jbc.M800503200
DOI:10.1002/cbic.200500504
https://mibig.secondarymetabolites.org/repository/BGC0000821.5/BGC0000821.gbk
https://www.uniprot.org/uniprotkb/Q8KZ94
https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv
  • reference
    DOI:10.1074/jbc.M800503200
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    RebM catalyzes glucosyl C-4′ O-methylation as the final step in rebeccamycin biosynthesis
    notes
    Singh et al. expressed Lechevalieria aerocolonigenes RebM from the pCST28aRebM construct, crystallized the enzyme, and analyzed SAM-dependent O-methyltransferase catalysis by the wild type enzyme and site-directed mutants.
  • reference
    DOI:10.1002/cbic.200500504
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    in vitro RebM-catalyzed 4′-O-methylation
    notes
    Zhang et al. established that rebM encodes the rebeccamycin 4'-O-methyltransferase and showed in vitro RebM methylation of RebG-derived indolocarbazole glucosides.
  • reference
    https://mibig.secondarymetabolites.org/repository/BGC0000821.5/BGC0000821.gbk
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    MIBiG BGC0000821.5 maps the L. aerocolonigenes AB090952 rebeccamycin biosynthetic gene cluster CDS BAC10678.1 to rebM.
  • reference
    https://www.uniprot.org/uniprotkb/Q8KZ94
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    Reviewed UniProtKB:Q8KZ94 is the 283 aa L. aerocolonigenes RebM demethylrebeccamycin-D-glucose O-methyltransferase, cross-references AB090952 protein BAC10678.1, and annotates RHEA:27353 from PMID:18502766.
  • reference
    https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    The Rhea Swiss-Prot mapping links UniProtKB:Q8KZ94 to the RebM O-methyltransferase reaction RHEA:27353.

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

Causal graph — biosynthesis 3 nodes, 2 edges

Partial L. aerocolonigenes rebeccamycin biosynthesis graph for RebG-catalyzed N-glycosylation.

SubjectPredicateObjectNotesEvidence
dichloroarcyriaflavin A is N-glycosylated by RebG 4'-demethylrebeccamycin synthase RebG N-glucosylates the indolocarbazole aglycone dichloroarcyriaflavin A.
DOI:10.1002/cbic.200500504
DOI:10.1271/bbb.67.127
https://mibig.secondarymetabolites.org/repository/BGC0000821.5/BGC0000821.gbk
https://www.uniprot.org/uniprotkb/Q8KHE4
https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv
  • reference
    DOI:10.1002/cbic.200500504
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    rebG encodes for the rebeccamycin N-glucosyltransferase
    notes
    Zhang et al. used in vivo RebG biotransformation in Streptomyces lividans and Escherichia coli and characterized indolocarbazole glucosylation by L. aerocolonigenes RebG.
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT
    notes
    Onaka et al. characterized the L. aerocolonigenes ATCC 39243 reb cluster and assigned RebG to D-glucose glycosylation of the rebeccamycin aglycon.
  • reference
    https://mibig.secondarymetabolites.org/repository/BGC0000821.5/BGC0000821.gbk
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    MIBiG BGC0000821.5 maps the L. aerocolonigenes AB090952 rebeccamycin biosynthetic gene cluster CDS BAC10673.1 to rebG and annotates the product as an N-glycosyltransferase.
  • reference
    https://www.uniprot.org/uniprotkb/Q8KHE4
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    Reviewed UniProtKB:Q8KHE4 is the 421 aa L. aerocolonigenes RebG 4'-demethylrebeccamycin synthase, cross-references AB090952 protein BAC10673.1, and annotates RHEA:27397 from PMID:16575939.
  • reference
    https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    The Rhea Swiss-Prot mapping links UniProtKB:Q8KHE4 to RHEA:27397, the EC 4.3.3.5 reaction interconverting dichloroarcyriaflavin A and 4'-demethylrebeccamycin.
RebG 4'-demethylrebeccamycin synthase forms 4'-demethylrebeccamycin The RebG-catalyzed reaction yields 4'-demethylrebeccamycin for terminal methylation by RebM.
DOI:10.1002/cbic.200500504
DOI:10.1271/bbb.67.127
https://mibig.secondarymetabolites.org/repository/BGC0000821.5/BGC0000821.gbk
https://www.uniprot.org/uniprotkb/Q8KHE4
https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv
  • reference
    DOI:10.1002/cbic.200500504
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    rebG encodes for the rebeccamycin N-glucosyltransferase
    notes
    Zhang et al. used in vivo RebG biotransformation in Streptomyces lividans and Escherichia coli and characterized indolocarbazole glucosylation by L. aerocolonigenes RebG.
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT
    notes
    Onaka et al. characterized the L. aerocolonigenes ATCC 39243 reb cluster and assigned RebG to D-glucose glycosylation of the rebeccamycin aglycon.
  • reference
    https://mibig.secondarymetabolites.org/repository/BGC0000821.5/BGC0000821.gbk
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    MIBiG BGC0000821.5 maps the L. aerocolonigenes AB090952 rebeccamycin biosynthetic gene cluster CDS BAC10673.1 to rebG and annotates the product as an N-glycosyltransferase.
  • reference
    https://www.uniprot.org/uniprotkb/Q8KHE4
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    Reviewed UniProtKB:Q8KHE4 is the 421 aa L. aerocolonigenes RebG 4'-demethylrebeccamycin synthase, cross-references AB090952 protein BAC10673.1, and annotates RHEA:27397 from PMID:16575939.
  • reference
    https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-30
    notes
    The Rhea Swiss-Prot mapping links UniProtKB:Q8KHE4 to RHEA:27397, the EC 4.3.3.5 reaction interconverting dichloroarcyriaflavin A and 4'-demethylrebeccamycin.

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

Causal graph — biosynthesis 11 nodes, 10 edges

ATCC 39243 RebF/RebH reconstitution, not a demonstrated physical complex. Canonical parent IDs are retained with REVIEW_NEEDED for recombinant termini: printed reverse primers do not exactly match AB090952.1, AJ414559.1, AF534707.1 or AB071405.1. Neither a cloning mutation nor a paper typo is resolved.

SubjectPredicateObjectNotesEvidence
FAD is substrate for NADH-dependent FAD reduction
DOI:10.1073/pnas.0500755102
  • reference
    DOI:10.1073/pnas.0500755102
    evidence type
    PRIMARY_EXPERIMENT
NADH supplies reducing equivalents to NADH-dependent FAD reduction
DOI:10.1073/pnas.0500755102
  • reference
    DOI:10.1073/pnas.0500755102
    evidence type
    PRIMARY_EXPERIMENT
N-His-RebF assay construct catalyzes NADH-dependent FAD reduction N-His pET28a construct from ATCC 39243 genomic DNA, expressed in E. coli BL21(DE3). Assayed by NADH absorbance loss at 340 nm; NADPH was not accepted under tested conditions.
DOI:10.1073/pnas.0500755102
https://www.uniprot.org/uniprotkb/Q8KI76
  • reference
    DOI:10.1073/pnas.0500755102
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    NADPH was not accepted for oxidation by RebF.
  • reference
    https://www.uniprot.org/uniprotkb/Q8KI76
    evidence type
    DATABASE_ASSERTION
    notes
    170-aa canonical rebF parent exactly matches AB090952.1 CDS BAC10680.1; taxon 68170 (Lentzea, formerly Lechevalieria/Saccharothrix aerocolonigenes). Canonical accession excludes purification tags.
    retrieved on
    2026-10-03
NADH-dependent FAD reduction produces Reduced FAD
DOI:10.1073/pnas.0500755102
  • reference
    DOI:10.1073/pnas.0500755102
    evidence type
    PRIMARY_EXPERIMENT
Reduced FAD supports In-vitro tryptophan 7-chlorination FMN supported isolated RebF activity but not coupled chlorination; no direct protein interaction inferred.
DOI:10.1073/pnas.0500755102
  • reference
    DOI:10.1073/pnas.0500755102
    evidence type
    PRIMARY_EXPERIMENT
L-tryptophan is substrate for In-vitro tryptophan 7-chlorination
DOI:10.1073/pnas.0500755102
  • reference
    DOI:10.1073/pnas.0500755102
    evidence type
    PRIMARY_EXPERIMENT
Molecular oxygen is required in In-vitro tryptophan 7-chlorination
DOI:10.1073/pnas.0500755102
  • reference
    DOI:10.1073/pnas.0500755102
    evidence type
    PRIMARY_EXPERIMENT
Chloride is incorporated during In-vitro tryptophan 7-chlorination
DOI:10.1073/pnas.0500755102
  • reference
    DOI:10.1073/pnas.0500755102
    evidence type
    PRIMARY_EXPERIMENT
N-His-RebH assay construct catalyzes In-vitro tryptophan 7-chlorination N-His pET28a/BL21(DE3) construct. Radio-TLC assays used 1 uM RebH, 3 uM RebF, 100 uM FAD, 10 mM NADH and 10 mM NaCl. Ratio is an assay optimum, not complex stoichiometry.
DOI:10.1073/pnas.0500755102
https://www.uniprot.org/uniprotkb/Q8KHZ8
  • reference
    DOI:10.1073/pnas.0500755102
    evidence type
    PRIMARY_EXPERIMENT
  • reference
    https://www.uniprot.org/uniprotkb/Q8KHZ8
    evidence type
    DATABASE_ASSERTION
    notes
    530-aa canonical rebH parent exactly matches AB090952.1 CDS BAC10682.1; taxon 68170 (Lentzea, formerly Lechevalieria/Saccharothrix aerocolonigenes). Canonical accession excludes purification tags.
    retrieved on
    2026-10-03
In-vitro tryptophan 7-chlorination produces 7-chloro-L-tryptophan Radio-HPLC, isotope incorporation, MALDI-MS and NMR versus authentic standard support the product.
DOI:10.1073/pnas.0500755102
  • reference
    DOI:10.1073/pnas.0500755102
    evidence type
    PRIMARY_EXPERIMENT

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

Causal graph — biosynthesis 8 nodes, 8 edges

RebO endpoint assays distinguish chlorinated and unchlorinated substrates. Keto acids are recovered assay products, not assertions that native RebD receives free keto acid instead of the imine intermediate. The enzyme carries noncovalently bound FAD, not the FMN/iron combination in the MITE lead.

SubjectPredicateObjectNotesEvidence
L-tryptophan is substrate for RebO unchlorinated-substrate assay
DOI:10.1128/JB.187.6.2084-2092.2005
  • reference
    DOI:10.1128/JB.187.6.2084-2092.2005
    evidence type
    PRIMARY_EXPERIMENT
C-His-RebO assay construct catalyzes RebO unchlorinated-substrate assay pDHS5514/pET24b from CLA14 cosmid, ATCC 39243. C-terminal KLAAALEHHHHHH extension retained; chaperone-assisted E. coli expression. Published primer target regions match AB090952.1.
DOI:10.1128/JB.187.6.2084-2092.2005
https://www.uniprot.org/uniprotkb/Q8KHS0
  • reference
    DOI:10.1128/JB.187.6.2084-2092.2005
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    contains a noncovalently bound FAD cofactor
  • reference
    https://www.uniprot.org/uniprotkb/Q8KHS0
    evidence type
    DATABASE_ASSERTION
    notes
    473-aa canonical rebO parent exactly matches AB090952.1 CDS BAC10674.1; taxon 68170 (Lentzea, formerly Lechevalieria/Saccharothrix aerocolonigenes). Canonical accession excludes purification tags.
    retrieved on
    2026-10-03
RebO unchlorinated-substrate assay yields recovered Indole-3-pyruvic acid HPLC/co-injection and UV comparison. 0.2 mM L-Trp, 100 U catalase, pH 8.0, 28 C, 4-5 h; Figure 5 uses 1 uM RebO.
DOI:10.1128/JB.187.6.2084-2092.2005
  • reference
    DOI:10.1128/JB.187.6.2084-2092.2005
    evidence type
    PRIMARY_EXPERIMENT
7-chloro-L-tryptophan is substrate for RebO chlorinated-substrate assay
DOI:10.1128/JB.187.6.2084-2092.2005
  • reference
    DOI:10.1128/JB.187.6.2084-2092.2005
    evidence type
    PRIMARY_EXPERIMENT
C-His-RebO assay construct catalyzes RebO chlorinated-substrate assay Table 1: 57-fold higher kcat/Km than L-Trp in the peroxide-coupled spectrophotometric assay; not exclusive specificity.
DOI:10.1128/JB.187.6.2084-2092.2005
  • reference
    DOI:10.1128/JB.187.6.2084-2092.2005
    evidence type
    PRIMARY_EXPERIMENT
RebO chlorinated-substrate assay yields recovered 7-chloro-indole-3-pyruvic acid HPLC/LC-MS versus standard after 3-4 h at 28 C, pH 8.0, 100 U catalase. RebO oxidation precedes imine hydrolysis; this is an endpoint observation.
DOI:10.1128/JB.187.6.2084-2092.2005
  • reference
    DOI:10.1128/JB.187.6.2084-2092.2005
    evidence type
    PRIMARY_EXPERIMENT
RebO unchlorinated-substrate assay generates Hydrogen peroxide Separate kinetic assay detects peroxide via horseradish peroxidase/o-dianisidine at 440 nm; catalase is included in product-isolation assays.
DOI:10.1128/JB.187.6.2084-2092.2005
  • reference
    DOI:10.1128/JB.187.6.2084-2092.2005
    evidence type
    PRIMARY_EXPERIMENT
RebO chlorinated-substrate assay generates Hydrogen peroxide
DOI:10.1128/JB.187.6.2084-2092.2005
  • reference
    DOI:10.1128/JB.187.6.2084-2092.2005
    evidence type
    PRIMARY_EXPERIMENT

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

Causal graph — biosynthesis 8 nodes, 8 edges

Separate RebO/RebD coupled reconstitutions from 7-chloro-L-tryptophan or L-tryptophan, not direct RebD turnover of an amino acid. SI pp. S4-S5: 0.5 uM RebO, 1 uM RebD, 100 U catalase, phosphate pH 7.6, 28.5 C, 6-15 h. Unchlorinated chromopyrrolic acid is an assay alternative, not the chlorinated precursor of this exact record.

SubjectPredicateObjectNotesEvidence
L-tryptophan is supplied to Unchlorinated RebO/RebD assay
DOI:10.1021/ja056749x.s001
  • reference
    DOI:10.1021/ja056749x.s001
    evidence type
    PRIMARY_EXPERIMENT
C-His-RebO assay construct contributes to Unchlorinated RebO/RebD assay RebO prepared as in the 2005 oxidase study; no obligate physical RebO/RebD complex asserted.
DOI:10.1021/ja056749x.s001
  • reference
    DOI:10.1021/ja056749x.s001
    evidence type
    PRIMARY_EXPERIMENT
His-tagged RebD assay construct contributes to Unchlorinated RebO/RebD assay SI pp. S1-S3: pDHS5525/pET24b from ATCC 39243 CLA14; His-tagged protein. Published primer target regions match the 1013-aa AB090952.1 RebD parent.
DOI:10.1021/ja056749x.s001
https://www.uniprot.org/uniprotkb/Q8KHV6
  • reference
    DOI:10.1021/ja056749x.s001
    evidence type
    PRIMARY_EXPERIMENT
  • reference
    https://www.uniprot.org/uniprotkb/Q8KHV6
    evidence type
    DATABASE_ASSERTION
    notes
    1013-aa canonical rebD parent exactly matches AB090952.1 CDS BAC10675.1; taxon 68170 (Lentzea, formerly Lechevalieria/Saccharothrix aerocolonigenes). Canonical accession excludes purification tags.
    retrieved on
    2026-10-03
Unchlorinated RebO/RebD assay produces Chromopyrrolic acid (8a) SI Figures 6-7: HPLC and MS/MS, [M-H]- 384.1.
DOI:10.1021/ja056749x.s001
  • reference
    DOI:10.1021/ja056749x.s001
    evidence type
    PRIMARY_EXPERIMENT
7-chloro-L-tryptophan is supplied to Chlorinated RebO/RebD assay
DOI:10.1021/ja056749x.s001
  • reference
    DOI:10.1021/ja056749x.s001
    evidence type
    PRIMARY_EXPERIMENT
C-His-RebO assay construct contributes to Chlorinated RebO/RebD assay
DOI:10.1021/ja056749x.s001
  • reference
    DOI:10.1021/ja056749x.s001
    evidence type
    PRIMARY_EXPERIMENT
His-tagged RebD assay construct contributes to Chlorinated RebO/RebD assay
DOI:10.1021/ja056749x.s001
  • reference
    DOI:10.1021/ja056749x.s001
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    in the presence of catalase
Chlorinated RebO/RebD assay produces 11,11'-dichlorochromopyrrolic acid (8b) SI Figures 4-5 call this chlorochromopyrrolic acid 8b; [M-H]- 452.0 and chlorine isotope pattern support the dichlorinated product from two chlorinated monomers.
DOI:10.1021/ja056749x.s001
DOI:10.1128/JB.187.6.2084-2092.2005
  • reference
    DOI:10.1021/ja056749x.s001
    evidence type
    PRIMARY_EXPERIMENT
  • reference
    DOI:10.1128/JB.187.6.2084-2092.2005
    evidence type
    PRIMARY_EXPERIMENT
    notes
    Figure 2 identifies the chlorinated dimer as 11,11'-dichlorochromopyrrolic acid.

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

Causal graph — biosynthesis 5 nodes, 4 edges

RebD assay supplied with indolepyruvic acid and ammonium, explicitly separated from a native substrate assignment. The tandem-study abstract favors the imine as substrate; this assay does not establish that free keto acid is directly cyclized without imine formation. No conversion of the chlorinated keto acid is inferred from this unchlorinated assay.

SubjectPredicateObjectNotesEvidence
Indole-3-pyruvic acid is supplied to Ammonium-supplemented RebD assay SI pp. S4-S5 and Figures 8-9; IPA dissolved in DMSO, ammonium sulfate 2.0-7.4 mM, pH 7.5.
DOI:10.1021/ja056749x.s001
  • reference
    DOI:10.1021/ja056749x.s001
    evidence type
    PRIMARY_EXPERIMENT
Ammonium is supplied to Ammonium-supplemented RebD assay
DOI:10.1021/ja056749x.s001
  • reference
    DOI:10.1021/ja056749x.s001
    evidence type
    PRIMARY_EXPERIMENT
His-tagged RebD assay construct catalyzes product formation in Ammonium-supplemented RebD assay
DOI:10.1021/ja056749x.s001
DOI:10.1021/bi051706e
  • reference
    DOI:10.1021/ja056749x.s001
    evidence type
    PRIMARY_EXPERIMENT
  • reference
    DOI:10.1021/bi051706e
    evidence type
    PRIMARY_EXPERIMENT
    notes
    Primary abstract specifies imino-indolepyruvate as the preferred RebD substrate; not evidence for direct keto-acid cyclization.
Ammonium-supplemented RebD assay produces Chromopyrrolic acid (8a) Figures 8-9: HPLC plus MS/MS with [M-H]- 384.1; this is a supplemented in-vitro result.
DOI:10.1021/ja056749x.s001
  • reference
    DOI:10.1021/ja056749x.s001
    evidence type
    PRIMARY_EXPERIMENT

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Causal graph — biosynthesis 5 nodes, 4 edges

ATCC 39243 genetic and feeding experiments. A disruption phenotype is not purified-RebP catalysis; the protein ID denotes the wild-type reference.

SubjectPredicateObjectNotesEvidence
ATCC 39243 rebP::kmr mutant has insertion disrupting the gene encoding RebP wild-type protein Single crossover, Southern-verified; both internal primer targets match AB071405.1 and AB090952.1.
DOI:10.1271/bbb.67.127
https://www.uniprot.org/uniprotkb/Q8KIC8
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT
  • reference
    https://www.uniprot.org/uniprotkb/Q8KIC8
    evidence type
    DATABASE_ASSERTION
    notes
    397-aa canonical wild-type parent matches AB071405.1/BAC15753.1 exactly; taxon 68170. This ID does not denote a disrupted allele or a purification tag.
    retrieved on
    2026-10-03
ATCC 39243 rebP::kmr mutant accumulates 11,11'-dichlorochromopyrrolic acid Figure 4D and Table 3; HPLC, NMR and MS support compound 4.
DOI:10.1271/bbb.67.127
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT
11,11'-dichlorochromopyrrolic acid is supplied to CCA feeding to the rebH::kmr culture
DOI:10.1271/bbb.67.127
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT
CCA feeding to the rebH::kmr culture yields detected rebeccamycin Figure 6: HPLC/UV detection after seven days; whole-cell conversion, not a single-enzyme assay.
DOI:10.1271/bbb.67.127
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT

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Causal graph — biosynthesis 8 nodes, 7 edges

ATCC 39243 mutant profiles, not a RebC substrate/product assignment. Protein IDs denote wild-type references. Products 6/7 are unresolved N-glycoside mixtures; 8/9 are not established pathway intermediates.

SubjectPredicateObjectNotesEvidence
ATCC 39243 in-frame rebC truncation has in-frame truncation of the gene encoding RebC wild-type protein
DOI:10.1271/bbb.67.127
https://www.uniprot.org/uniprotkb/Q8KI25
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT
  • reference
    https://www.uniprot.org/uniprotkb/Q8KI25
    evidence type
    DATABASE_ASSERTION
    notes
    529-aa canonical wild-type parent matches AB071405.1/BAC15752.1 exactly; taxon 68170. This ID does not denote a disrupted allele or a purification tag.
    retrieved on
    2026-10-03
ATCC 39243 in-frame rebC truncation accumulates Shunt glycoside mixtures 6 and 7 Figure 4E: unresolved 12-N/13-N glycosylation; no exact structure IDs assigned.
DOI:10.1271/bbb.67.127
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT
ATCC 39243 rebC truncation plus rebG::kmr has in-frame truncation of the gene encoding RebC wild-type protein
DOI:10.1271/bbb.67.127
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT
ATCC 39243 rebC truncation plus rebG::kmr has insertion disrupting the gene encoding RebG wild-type protein
DOI:10.1271/bbb.67.127
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT
ATCC 39243 rebC truncation plus rebG::kmr accumulates dichloroarcyriaflavin A Figure 4F, compound 5; aglycone remains detectable without intact rebC.
DOI:10.1271/bbb.67.127
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT
ATCC 39243 rebC truncation plus rebG::kmr accumulates 7-deoxo-7-hydroxyrebeccamycin aglycone (8) NMR-assigned; feeding 8 or 9 did not yield rebeccamycin.
DOI:10.1271/bbb.67.127
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    neither compound was converted to rebeccamycin
ATCC 39243 rebC truncation plus rebG::kmr accumulates 7-deoxorebeccamycin aglycone (9)
DOI:10.1271/bbb.67.127
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT

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Causal graph — biosynthesis 3 nodes, 2 edges

Native-host requirement evidence for RebR. No promoter binding or direct transcriptional target was measured here.

SubjectPredicateObjectNotesEvidence
ATCC 39243 in-frame rebR truncation has in-frame truncation of the gene encoding RebR wild-type protein
DOI:10.1271/bbb.67.127
https://www.uniprot.org/uniprotkb/Q8KHD3
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT
  • reference
    https://www.uniprot.org/uniprotkb/Q8KHD3
    evidence type
    DATABASE_ASSERTION
    notes
    923-aa canonical wild-type parent matches AB071405.1/BAC15755.1 exactly; taxon 68170. This ID does not denote a disrupted allele or a purification tag.
    retrieved on
    2026-10-03
ATCC 39243 in-frame rebR truncation shows Rebeccamycin-related products undetected Figure 4I, HPLC/UV; G134 medium, 30 C, 11-day fermentation.
DOI:10.1271/bbb.67.127
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT

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Causal graph — biosynthesis 7 nodes, 6 edges

Partial comparison of contrasting native-production and engineered-host RebT phenotypes. The rebT-lacking construct and its no-transformant outcome form an intentionally disconnected experimental arm: neither source establishes a causal link between that arm and the other tested genotypes. Neither experiment directly measures transport; no universal production requirement, secretion mechanism or purified-protein activity is asserted.

SubjectPredicateObjectNotesEvidence
ATCC 39243 rebT::kmr mutant has insertion disrupting the gene encoding RebT wild-type protein Internal primers match AB090952.1 rebT; AB071405.1 does not contain this CDS.
DOI:10.1271/bbb.67.127
https://www.uniprot.org/uniprotkb/Q8KHB7
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT
  • reference
    https://www.uniprot.org/uniprotkb/Q8KHB7
    evidence type
    DATABASE_ASSERTION
    notes
    473-aa canonical wild-type parent matches AB090952.1/BAC10683.1 exactly; taxon 68170. This ID does not denote a disrupted allele or a purification tag.
    retrieved on
    2026-10-03
ATCC 39243 rebT::kmr mutant retains Native-host production assay HPLC: mutant 52.6 +/- 1 versus wild type 52.5 +/- 7 mg/L at nine days, as reported.
DOI:10.1271/bbb.67.127
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT
Native-host production assay produces rebeccamycin
DOI:10.1271/bbb.67.127
  • reference
    DOI:10.1271/bbb.67.127
    evidence type
    PRIMARY_EXPERIMENT
rebODCPGMH construct in S. albus J1074 yielded No transformants recovered Failure to recover transformants, not a measured killing rate or direct transport assay.
DOI:10.1073/pnas.0407809102
  • reference
    DOI:10.1073/pnas.0407809102
    evidence type
    PRIMARY_EXPERIMENT
rebODCPGMH plus rebT construct in S. albus J1074 includes a gene encoding RebT wild-type protein ATCC 39243 gene donor; canonical parent ID, not a verified full recombinant construct sequence.
DOI:10.1073/pnas.0407809102
  • reference
    DOI:10.1073/pnas.0407809102
    evidence type
    PRIMARY_EXPERIMENT
rebODCPGMH plus rebT construct in S. albus J1074 yields transformants producing rebeccamycin R5A medium; HPLC-MS, Table 2 compound 12. The genotype includes the biosynthetic enzymes.
DOI:10.1073/pnas.0407809102
  • reference
    DOI:10.1073/pnas.0407809102
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    only when rebT was also added to the gene combinations

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Causal graph — biosynthesis 5 nodes, 4 edges

S. albus J1074 coexpressing ATCC 39243 rebCP converts fed, unchlorinated chromopyrrolic acid. This is a surrogate whole-cell assay, not formation of the chlorinated native aglycone by isolated proteins.

SubjectPredicateObjectNotesEvidence
RebC wild-type protein contributes in the expressed gene combination to rebCP whole-cell feeding assay Canonical gene-product reference; not a claim of a purified RebC/RebP complex.
DOI:10.1073/pnas.0407809102
  • reference
    DOI:10.1073/pnas.0407809102
    evidence type
    PRIMARY_EXPERIMENT
RebP wild-type protein contributes in the expressed gene combination to rebCP whole-cell feeding assay
DOI:10.1073/pnas.0407809102
  • reference
    DOI:10.1073/pnas.0407809102
    evidence type
    PRIMARY_EXPERIMENT
Unchlorinated chromopyrrolic acid is fed to rebCP whole-cell feeding assay
DOI:10.1073/pnas.0407809102
  • reference
    DOI:10.1073/pnas.0407809102
    evidence type
    PRIMARY_EXPERIMENT
rebCP whole-cell feeding assay produces Unchlorinated arcyriaflavin A Product assignment by HPLC retention, UV and MS; Table 2 compound 2.
DOI:10.1073/pnas.0407809102
  • reference
    DOI:10.1073/pnas.0407809102
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    We also produced arcyriaflavin by feeding chromopyrrolic acid

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Causal graph — biosynthesis 3 nodes, 2 edges

RebC structural binding evidence with unchlorinated ligands. The captured ligand was modeled as 7-carboxy-K252c, potentially a tautomer mixture; direct substrate turnover was not established.

SubjectPredicateObjectNotesEvidence
N-His-RebC crystallization construct contains bound FAD PDB 2R0G chains A/B: 529-aa canonical Q8KI25 plus N-terminal MGSSHHHHHHSSGLVPRGSH, 549 aa total; tag disordered. Two chains in the asymmetric unit do not imply an obligate dimer.
DOI:10.1073/pnas.0707190104
https://www.rcsb.org/structure/2R0G
  • reference
    DOI:10.1073/pnas.0707190104
    evidence type
    PRIMARY_EXPERIMENT
  • reference
    https://www.rcsb.org/structure/2R0G
    evidence type
    DATABASE_ASSERTION
    notes
    Deposited polymer sequence exactly matches the canonical parent after its 20-aa tag.
    retrieved on
    2026-10-03
N-His-RebC crystallization construct binds ligand modeled as Ligand modeled as 7-carboxy-K252c Week-long chromopyrrolic-acid soak; density fits the degradation intermediate, not supplied CPA. FAD is IN in this structure. Binding is not proof of hydroxylation.
DOI:10.1073/pnas.0707190104
  • reference
    DOI:10.1073/pnas.0707190104
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    the spontaneous decomposition of 7-carboxy-K252c has precluded direct testing

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Explore across X-Mech

AntibioticMech (rebeccamycin) ↗ MediaIngredientMech (CHEBI:135511) ↗ TaxonMech: Lechevalieria aerocolonigenes (NCBITaxon:68170) ↗ PathwayMech (mibig:BGC0000821) ↗

Provenance

Source conceptSourceVersion
BGC0000821MIBIG5
CHEBI:135511CHEBI3-star

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