violacein

CHEBI:131914 EXACT SEEDED antibacterial

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 hydroxyindoles resulting from the formal oxidative coupling between the 3-position of 1,3-dihydro-2H-indol-2-one and the 3-position of 1,3-dihydro-2H-pyrrol-2-one, which is substituted at the 5 position by a 5-hydroxy-1H-indol-3-yl group, where the newly-formed double bond has E configuration. It is a purple chromobacterial pigment that has antibacterial, antifungal, antiprotozoan, and anticancer properties.

Structure

Standard InChIKey	XAPNKXIRQFHCHN-QGOAFFKASA-N
SMILES	C1=CC=C2C(=C1)/C(=C\3/C=C(NC3=O)C4=CNC5=C4C=C(C=C5)O)/C(=O)N2
Stereochemistry	fully defined
Cross-references	pubchem:9928039

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
Duganella sp. B2 NCBITaxon:445969	SOURCE_ASSERTION	mibig:BGC0000831	PMID:22391969

Occurrences 4

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
Pseudoalteromonas tunicata NCBITaxon:314281	LOTUS	DOI:10.3390/10101286
Chromobacterium violaceum NCBITaxon:536	LOTUS	DOI:10.1021/BI061998Z
Chromobacterium violaceum NCBITaxon:536	CHEBI	PMID:17176066
Escherichia coli NCBITaxon:562	LOTUS	DOI:10.1021/OL0509585

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000831	Duganella sp. B2 NCBITaxon:445969	CLUSTER_UNSTATED	genbank:GQ266676.1

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	VioD protodeoxyviolaceinate monooxygenase UniProtKB:Q9S3U8	RHEA:49372	CHEBI:90907 → CHEBI:90898	DOI:10.1021/bi061998z
2	VioC violacein synthase UniProtKB:Q9S3U9	RHEA:49120	CHEBI:90898 → CHEBI:90900	DOI:10.1021/bi061998z

Step 1: This partial Chromobacterium violaceum VioD/VioC pathway follows the enzymatic carboxylate branch from protodeoxyviolaceinate to protoviolaceinate, rather than the downstream neutral proviolacein scaffold.

Step 2: This curated step stops at RHEA:49120 violaceinate. The later connection to neutral CHEBI:131914 violacein is left unexpanded because no exact enzymatic Rhea reaction connects the carboxylate and pyrrolidone forms.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 5 nodes, 4 edges

Partial Chromobacterium violaceum VioD/VioC enzymatic carboxylate branch from protodeoxyviolaceinate to violaceinate.

Subject	Predicate	Object	Notes	Evidence
protodeoxyviolaceinate	is hydroxylated by	VioD	VioD catalyzes the RHEA:49372 hydroxylation of protodeoxyviolaceinate to protoviolaceinate.	DOI:10.1021/bi061998z DOI:10.1039/b705358d https://www.uniprot.org/uniprotkb/Q9S3U8 reference DOI:10.1021/bi061998z evidence type PRIMARY_EXPERIMENT snippet purified five contiguously encoded proteins VioA-E after expression in Escherichia coli notes Balibar and Walsh reconstituted Chromobacterium violaceum VioA-E in vitro and demonstrated that the VioD then VioC flavin-dependent oxygenase sequence completes the late violacein pathway. reference DOI:10.1039/b705358d evidence type PRIMARY_EXPERIMENT snippet A biosynthetic intermediate of violacein produced by the mixed enzymes of VioABDE notes Shinoda et al. identified protoviolaceinic acid as the VioABDE product and showed that VioC oxygenates the right-side indole ring in the final enzymatic step. reference https://www.uniprot.org/uniprotkb/Q9S3U8 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes Reviewed UniProtKB:Q9S3U8 is Chromobacterium violaceum strain ATCC 12472/JCM 1249 VioD, gene vioD/CV_3271, cross-references EMBL AF172851 protein AAD51811.1, EMBL AB032799 protein BAA84785.1, and EMBL AE016825 protein AAQ60935.1, and annotates RHEA:49372.
VioD	forms	protoviolaceinate	The VioD carboxylate product is the major pH 7.3 microspecies of protoviolaceinic acid.	DOI:10.1021/bi061998z DOI:10.1039/b705358d https://www.uniprot.org/uniprotkb/Q9S3U8 reference DOI:10.1021/bi061998z evidence type PRIMARY_EXPERIMENT snippet purified five contiguously encoded proteins VioA-E after expression in Escherichia coli notes Balibar and Walsh reconstituted Chromobacterium violaceum VioA-E in vitro and demonstrated that the VioD then VioC flavin-dependent oxygenase sequence completes the late violacein pathway. reference DOI:10.1039/b705358d evidence type PRIMARY_EXPERIMENT snippet A biosynthetic intermediate of violacein produced by the mixed enzymes of VioABDE notes Shinoda et al. identified protoviolaceinic acid as the VioABDE product and showed that VioC oxygenates the right-side indole ring in the final enzymatic step. reference https://www.uniprot.org/uniprotkb/Q9S3U8 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes Reviewed UniProtKB:Q9S3U8 is Chromobacterium violaceum strain ATCC 12472/JCM 1249 VioD, gene vioD/CV_3271, cross-references EMBL AF172851 protein AAD51811.1, EMBL AB032799 protein BAA84785.1, and EMBL AE016825 protein AAQ60935.1, and annotates RHEA:49372.
protoviolaceinate	is hydroxylated by	VioC	VioC catalyzes the RHEA:49120 hydroxylation of protoviolaceinate to violaceinate.	DOI:10.1021/bi061998z DOI:10.1039/b705358d https://www.uniprot.org/uniprotkb/Q9S3U9 reference DOI:10.1021/bi061998z evidence type PRIMARY_EXPERIMENT snippet purified five contiguously encoded proteins VioA-E after expression in Escherichia coli notes Balibar and Walsh reconstituted Chromobacterium violaceum VioA-E in vitro and demonstrated that the VioD then VioC flavin-dependent oxygenase sequence completes the late violacein pathway. reference DOI:10.1039/b705358d evidence type PRIMARY_EXPERIMENT snippet A biosynthetic intermediate of violacein produced by the mixed enzymes of VioABDE notes Shinoda et al. identified protoviolaceinic acid as the VioABDE product and showed that VioC oxygenates the right-side indole ring in the final enzymatic step. reference https://www.uniprot.org/uniprotkb/Q9S3U9 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes Reviewed UniProtKB:Q9S3U9 is Chromobacterium violaceum strain ATCC 12472/JCM 1249 VioC, gene vioC/CV_3272, cross-references EMBL AF172851 protein AAD51810.1, EMBL AB032799 protein BAA84784.1, and EMBL AE016825 protein AAQ60936.1, and annotates RHEA:49120.
VioC	forms	violaceinate	The VioC carboxylate product is violaceinate rather than neutral violacein.	DOI:10.1021/bi061998z DOI:10.1039/b705358d https://www.uniprot.org/uniprotkb/Q9S3U9 reference DOI:10.1021/bi061998z evidence type PRIMARY_EXPERIMENT snippet purified five contiguously encoded proteins VioA-E after expression in Escherichia coli notes Balibar and Walsh reconstituted Chromobacterium violaceum VioA-E in vitro and demonstrated that the VioD then VioC flavin-dependent oxygenase sequence completes the late violacein pathway. reference DOI:10.1039/b705358d evidence type PRIMARY_EXPERIMENT snippet A biosynthetic intermediate of violacein produced by the mixed enzymes of VioABDE notes Shinoda et al. identified protoviolaceinic acid as the VioABDE product and showed that VioC oxygenates the right-side indole ring in the final enzymatic step. reference https://www.uniprot.org/uniprotkb/Q9S3U9 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes Reviewed UniProtKB:Q9S3U9 is Chromobacterium violaceum strain ATCC 12472/JCM 1249 VioC, gene vioC/CV_3272, cross-references EMBL AF172851 protein AAD51810.1, EMBL AB032799 protein BAA84784.1, and EMBL AE016825 protein AAQ60936.1, and annotates RHEA:49120.

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

Elsewhere in the fleet

AntibioticMech — CHEBI:131914 (same structure, same inchikey)

Explore across X-Mech

AntibioticMech (violacein) ↗ MediaIngredientMech (CHEBI:131914) ↗ TaxonMech: Duganella sp. B2 (NCBITaxon:445969) ↗ PathwayMech (mibig:BGC0000831) ↗

Provenance

Source concept	Source	Version
BGC0000831	MIBIG	3
CHEBI:131914	CHEBI	3-star

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