agrobactin

naturalproductmech:mibig-bb581c6679 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	BWPMKVHHFNGYEN-CJAUYULYSA-N
SMILES	C[C@@H]1[C@H](N=C(O1)C2=C(C(=CC=C2)O)O)C(=O)N(CCCCNC(=O)C3=C(C(=CC=C3)O)O)CCCNC(=O)C4=C(C(=CC=C4)O)O
Stereochemistry	fully defined
Cross-references	npatlas:NPA018820

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 nrps, 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
Agrobacterium tumefaciens NCBITaxon:358	BGC_CHARACTERIZED	mibig:BGC0002474	PMID:12207035

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
Rhizobium radiobacter NCBITaxon:362	LOTUS	DOI:10.1021/JA00546A014
Rhizobium radiobacter NCBITaxon:362	LOTUS	DOI:10.1266/GGS.77.137
Agrobacterium tumefaciens NCBITaxon:358	LOTUS	DOI:10.1021/JA00546A014
Agrobacterium tumefaciens NCBITaxon:358	LOTUS	DOI:10.1266/GGS.77.137

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0002474	Agrobacterium tumefaciens NCBITaxon:358	CLUSTER_DEMONSTRATED	genbank:AB083344.2

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	AgbC isochorismate synthase UniProtKB:Q8GRA0	RHEA:18985	CHEBI:29748 → CHEBI:29780	DOI:10.1266/ggs.77.137
2	AgbB isochorismatase UniProtKB:Q8GR98	RHEA:11112	CHEBI:29780 → CHEBI:58764	DOI:10.1266/ggs.77.137
3	AgbA 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase UniProtKB:Q8GR97	RHEA:23824	CHEBI:58764 → CHEBI:36654	DOI:10.1266/ggs.77.137
4	AgbD phosphopantetheinyl transferase UniProtKB:Q83VM4		ungrounded → ungrounded	https://www.ncbi.nlm.nih.gov/nuccore/AB083344.2
5	AgbE 2,3-dihydroxybenzoate-AMP ligase UniProtKB:Q8GR99		ungrounded → ungrounded	DOI:10.1266/ggs.77.137
6	AgbF probable non-ribosomal peptide synthase UniProtKB:Q83VM5		ungrounded → ungrounded	https://www.ncbi.nlm.nih.gov/nuccore/AB083344.2

Step 1: AgbC is the AB083344.2 isochorismate synthase candidate; the reaction class is assigned from the UniProtKB/ARBA prediction rather than from a purified AgbC assay.

Step 2: AgbB is the AB083344.2 isochorismatase candidate required for catechol-compound production under iron limitation; the exact Rhea isochorismatase reaction is a UniProtKB/ARBA prediction.

Step 3: AgbA is the AB083344.2 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase candidate; the reaction class is assigned from the UniProtKB/ARBA prediction rather than from a purified AgbA assay.

Step 4: AgbD is the AB083344.2 phosphopantetheinyl-transferase candidate that would activate the aryl/peptidyl carrier proteins for 2,3-DHBA transfer and NRPS assembly.

Step 5: AgbE is the AB083344.2 2,3-dihydroxybenzoate-AMP ligase candidate that likely activates 2,3-DHBA for aryl-carrier-protein transfer.

Step 6: AgbF is the AB083344.2 probable NRPS candidate. The complete route from 2,3-DHBA to the catecholate siderophore agrobactin is left unresolved because individual thioester intermediates and the terminal product-forming steps were not resolved in the inspected sources.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 11 nodes, 10 edges

Partial Agrobacterium tumefaciens MAFF301001 agrobactin biosynthesis graph for proposed AB083344.2 AgbC/AgbB/AgbA 2,3-DHBA supply and proposed AgbD/AgbE/AgbF NRPS assembly contributions.

Subject	Predicate	Object	Notes	Evidence
chorismate(2-)	is proposed to be isomerized by	AgbC	AgbC is proposed to isomerize chorismate from AB083344.2, MIBiG, UniProtKB/ARBA, and GenPept annotations rather than a purified AgbC assay.	DOI:10.1266/ggs.77.137 https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html https://www.uniprot.org/uniprotkb/Q8GRA0 https://www.ncbi.nlm.nih.gov/protein/BAC16757.2 reference DOI:10.1266/ggs.77.137 evidence type PRIMARY_EXPERIMENT snippet We named these genes agb, after agrobactin. notes Sonoda et al. cloned Agrobacterium tumefaciens MAFF301001 fosmid 1A3 and identified agbC, agbE, agbB, and agbA in an operon involved in ferric iron uptake. reference https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes MIBiG BGC0002474.2 lists agrobactin as the product of the Agrobacterium tumefaciens AB083344.2 cluster and annotates AgbC/BAC16757.2 in that cluster. reference https://www.uniprot.org/uniprotkb/Q8GRA0 evidence type DATABASE_ASSERTION snippet DR EMBL; AB083344; BAC16757.2; -; Genomic_DNA. retrieved on 2026-09-28 notes Unreviewed UniProtKB:Q8GRA0 is Agrobacterium tumefaciens AgbC, length 342 aa, and cross-references EMBL AB083344 protein BAC16757.2. reference https://www.ncbi.nlm.nih.gov/protein/BAC16757.2 evidence type DATABASE_ASSERTION snippet probable isochorismate synthase retrieved on 2026-09-28 notes NCBI GenPept BAC16757.2 is the AB083344.2:1949..2977 AgbC coding sequence from Agrobacterium tumefaciens strain MAFF301001.
AgbC	is proposed to form	isochorismate(2-)	Isochorismate formation by AgbC is proposed from AB083344.2, MIBiG, UniProtKB/ARBA, and GenPept annotations rather than a purified AgbC assay.	DOI:10.1266/ggs.77.137 https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html https://www.uniprot.org/uniprotkb/Q8GRA0 https://www.ncbi.nlm.nih.gov/protein/BAC16757.2 reference DOI:10.1266/ggs.77.137 evidence type PRIMARY_EXPERIMENT snippet We named these genes agb, after agrobactin. notes Sonoda et al. cloned Agrobacterium tumefaciens MAFF301001 fosmid 1A3 and identified agbC, agbE, agbB, and agbA in an operon involved in ferric iron uptake. reference https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes MIBiG BGC0002474.2 lists agrobactin as the product of the Agrobacterium tumefaciens AB083344.2 cluster and annotates AgbC/BAC16757.2 in that cluster. reference https://www.uniprot.org/uniprotkb/Q8GRA0 evidence type DATABASE_ASSERTION snippet DR EMBL; AB083344; BAC16757.2; -; Genomic_DNA. retrieved on 2026-09-28 notes Unreviewed UniProtKB:Q8GRA0 is Agrobacterium tumefaciens AgbC, length 342 aa, and cross-references EMBL AB083344 protein BAC16757.2. reference https://www.ncbi.nlm.nih.gov/protein/BAC16757.2 evidence type DATABASE_ASSERTION snippet probable isochorismate synthase retrieved on 2026-09-28 notes NCBI GenPept BAC16757.2 is the AB083344.2:1949..2977 AgbC coding sequence from Agrobacterium tumefaciens strain MAFF301001.
isochorismate(2-)	is proposed to be hydrolyzed by	AgbB	AgbB is proposed to hydrolyze isochorismate; agbB mutagenesis showed catechol-compound production requires this gene but did not isolate this reaction.	DOI:10.1266/ggs.77.137 https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html https://www.uniprot.org/uniprotkb/Q8GR98 https://www.ncbi.nlm.nih.gov/protein/BAC16759.1 reference DOI:10.1266/ggs.77.137 evidence type PRIMARY_EXPERIMENT snippet Mutation analysis of agbB revealed that it is essential notes Sonoda et al. linked agbB to growth and catechol-compound production in iron-limiting medium in Agrobacterium tumefaciens MAFF301001. reference https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes MIBiG BGC0002474.2 lists agrobactin as the product of the Agrobacterium tumefaciens AB083344.2 cluster and annotates AgbB/BAC16759.1 in that cluster. reference https://www.uniprot.org/uniprotkb/Q8GR98 evidence type DATABASE_ASSERTION snippet DR EMBL; AB083344; BAC16759.1; -; Genomic_DNA. retrieved on 2026-09-28 notes Unreviewed UniProtKB:Q8GR98 is Agrobacterium tumefaciens AgbB, length 289 aa, and cross-references EMBL AB083344 protein BAC16759.1. reference https://www.ncbi.nlm.nih.gov/protein/BAC16759.1 evidence type DATABASE_ASSERTION snippet probable 2,3-dihydro-2,3-dihydroxybenzoate synthetase, isochorismatase protein retrieved on 2026-09-28 notes NCBI GenPept BAC16759.1 is the AB083344.2:4860..5729 AgbB coding sequence from Agrobacterium tumefaciens strain MAFF301001.
AgbB	is proposed to form	(2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate	Dihydro-DHB formation by AgbB is proposed; agbB mutagenesis showed catechol-compound production requires this gene but did not isolate this reaction.	DOI:10.1266/ggs.77.137 https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html https://www.uniprot.org/uniprotkb/Q8GR98 https://www.ncbi.nlm.nih.gov/protein/BAC16759.1 reference DOI:10.1266/ggs.77.137 evidence type PRIMARY_EXPERIMENT snippet Mutation analysis of agbB revealed that it is essential notes Sonoda et al. linked agbB to growth and catechol-compound production in iron-limiting medium in Agrobacterium tumefaciens MAFF301001. reference https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes MIBiG BGC0002474.2 lists agrobactin as the product of the Agrobacterium tumefaciens AB083344.2 cluster and annotates AgbB/BAC16759.1 in that cluster. reference https://www.uniprot.org/uniprotkb/Q8GR98 evidence type DATABASE_ASSERTION snippet DR EMBL; AB083344; BAC16759.1; -; Genomic_DNA. retrieved on 2026-09-28 notes Unreviewed UniProtKB:Q8GR98 is Agrobacterium tumefaciens AgbB, length 289 aa, and cross-references EMBL AB083344 protein BAC16759.1. reference https://www.ncbi.nlm.nih.gov/protein/BAC16759.1 evidence type DATABASE_ASSERTION snippet probable 2,3-dihydro-2,3-dihydroxybenzoate synthetase, isochorismatase protein retrieved on 2026-09-28 notes NCBI GenPept BAC16759.1 is the AB083344.2:4860..5729 AgbB coding sequence from Agrobacterium tumefaciens strain MAFF301001.
(2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate	is proposed to be oxidized by	AgbA	AgbA is proposed to oxidize 2,3-dihydro-2,3-dihydroxybenzoate from AB083344.2, MIBiG, UniProtKB/ARBA, and GenPept annotations rather than a purified AgbA assay.	DOI:10.1266/ggs.77.137 https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html https://www.uniprot.org/uniprotkb/Q8GR97 https://www.ncbi.nlm.nih.gov/protein/BAC16760.1 reference DOI:10.1266/ggs.77.137 evidence type PRIMARY_EXPERIMENT snippet We named these genes agb, after agrobactin. notes Sonoda et al. cloned Agrobacterium tumefaciens MAFF301001 fosmid 1A3 and identified agbC, agbE, agbB, and agbA in an operon involved in ferric iron uptake. reference https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes MIBiG BGC0002474.2 lists agrobactin as the product of the Agrobacterium tumefaciens AB083344.2 cluster and annotates AgbA/BAC16760.1 in that cluster. reference https://www.uniprot.org/uniprotkb/Q8GR97 evidence type DATABASE_ASSERTION snippet DR EMBL; AB083344; BAC16760.1; -; Genomic_DNA. retrieved on 2026-09-28 notes Unreviewed UniProtKB:Q8GR97 is Agrobacterium tumefaciens AgbA, length 251 aa, and cross-references EMBL AB083344 protein BAC16760.1. reference https://www.ncbi.nlm.nih.gov/protein/BAC16760.1 evidence type DATABASE_ASSERTION snippet probable 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase protein retrieved on 2026-09-28 notes NCBI GenPept BAC16760.1 is the AB083344.2:5743..6498 AgbA coding sequence from Agrobacterium tumefaciens strain MAFF301001.
AgbA	is proposed to form	2,3-dihydroxybenzoate	2,3-DHBA formation by AgbA is proposed from AB083344.2, MIBiG, UniProtKB/ARBA, and GenPept annotations rather than a purified AgbA assay.	DOI:10.1266/ggs.77.137 https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html https://www.uniprot.org/uniprotkb/Q8GR97 https://www.ncbi.nlm.nih.gov/protein/BAC16760.1 reference DOI:10.1266/ggs.77.137 evidence type PRIMARY_EXPERIMENT snippet We named these genes agb, after agrobactin. notes Sonoda et al. cloned Agrobacterium tumefaciens MAFF301001 fosmid 1A3 and identified agbC, agbE, agbB, and agbA in an operon involved in ferric iron uptake. reference https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes MIBiG BGC0002474.2 lists agrobactin as the product of the Agrobacterium tumefaciens AB083344.2 cluster and annotates AgbA/BAC16760.1 in that cluster. reference https://www.uniprot.org/uniprotkb/Q8GR97 evidence type DATABASE_ASSERTION snippet DR EMBL; AB083344; BAC16760.1; -; Genomic_DNA. retrieved on 2026-09-28 notes Unreviewed UniProtKB:Q8GR97 is Agrobacterium tumefaciens AgbA, length 251 aa, and cross-references EMBL AB083344 protein BAC16760.1. reference https://www.ncbi.nlm.nih.gov/protein/BAC16760.1 evidence type DATABASE_ASSERTION snippet probable 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase protein retrieved on 2026-09-28 notes NCBI GenPept BAC16760.1 is the AB083344.2:5743..6498 AgbA coding sequence from Agrobacterium tumefaciens strain MAFF301001.
AgbD	participates in	agrobactin NRPS assembly	AgbD is proposed to activate carrier-protein domains for agrobactin assembly.	https://www.ncbi.nlm.nih.gov/nuccore/AB083344.2 https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html https://www.uniprot.org/uniprotkb/Q83VM4 https://www.ncbi.nlm.nih.gov/protein/BAC57934.1 reference https://www.ncbi.nlm.nih.gov/nuccore/AB083344.2 evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes NCBI GenBank AB083344.2 is the 7,390 bp Agrobacterium tumefaciens MAFF301001 ferric iron uptake system gene cluster and annotates agbD/BAC57934.1. reference https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes MIBiG BGC0002474.2 lists agrobactin as the product of the Agrobacterium tumefaciens AB083344.2 cluster and annotates agbD/BAC57934.1 in that cluster. reference https://www.uniprot.org/uniprotkb/Q83VM4 evidence type DATABASE_ASSERTION snippet DR EMBL; AB083344; BAC57934.1; -; Genomic_DNA. retrieved on 2026-09-28 notes Unreviewed UniProtKB:Q83VM4 is Agrobacterium tumefaciens AgbD, length 241 aa, and cross-references EMBL AB083344 protein BAC57934.1. reference https://www.ncbi.nlm.nih.gov/protein/BAC57934.1 evidence type DATABASE_ASSERTION snippet probable phosphopantetheinyl transferase retrieved on 2026-09-28 notes NCBI GenPept BAC57934.1 is the AB083344.2:6529..7254 AgbD coding sequence from Agrobacterium tumefaciens strain MAFF301001.
2,3-dihydroxybenzoate	participates in	agrobactin NRPS assembly		DOI:10.1266/ggs.77.137 https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html https://www.ncbi.nlm.nih.gov/nuccore/AB083344.2 reference DOI:10.1266/ggs.77.137 evidence type PRIMARY_EXPERIMENT snippet We named these genes agb, after agrobactin. notes Sonoda et al. cloned Agrobacterium tumefaciens MAFF301001 fosmid 1A3 and identified agbC, agbE, agbB, and agbA in an operon involved in ferric iron uptake. reference https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes MIBiG BGC0002474.2 lists agrobactin as the product of the Agrobacterium tumefaciens AB083344.2 cluster and annotates agbF, agbC, agbE, agbB, agbA, and agbD in that cluster. reference https://www.ncbi.nlm.nih.gov/nuccore/AB083344.2 evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes NCBI GenBank AB083344.2 is the 7,390 bp Agrobacterium tumefaciens MAFF301001 ferric iron uptake system gene cluster and annotates agbF, agbC, agbE, agbB, agbA, and agbD.
AgbE	participates in	agrobactin NRPS assembly	AgbE is proposed to adenylate 2,3-DHBA for carrier-protein transfer.	DOI:10.1266/ggs.77.137 https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html https://www.uniprot.org/uniprotkb/Q8GR99 https://www.ncbi.nlm.nih.gov/protein/BAC16758.1 reference DOI:10.1266/ggs.77.137 evidence type PRIMARY_EXPERIMENT snippet We named these genes agb, after agrobactin. notes Sonoda et al. cloned Agrobacterium tumefaciens MAFF301001 fosmid 1A3 and identified agbC, agbE, agbB, and agbA in an operon involved in ferric iron uptake. reference https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes MIBiG BGC0002474.2 lists agrobactin as the product of the Agrobacterium tumefaciens AB083344.2 cluster and annotates AgbE/BAC16758.1 in that cluster. reference https://www.uniprot.org/uniprotkb/Q8GR99 evidence type DATABASE_ASSERTION snippet DR EMBL; AB083344; BAC16758.1; -; Genomic_DNA. retrieved on 2026-09-28 notes Unreviewed UniProtKB:Q8GR99 is Agrobacterium tumefaciens AgbE, length 541 aa, and cross-references EMBL AB083344 protein BAC16758.1. reference https://www.ncbi.nlm.nih.gov/protein/BAC16758.1 evidence type DATABASE_ASSERTION snippet probable 2,3-dihydroxybenzoate-AMP ligase protein retrieved on 2026-09-28 notes NCBI GenPept BAC16758.1 is the AB083344.2:3142..4767 AgbE coding sequence from Agrobacterium tumefaciens strain MAFF301001.
AgbF	participates in	agrobactin NRPS assembly	AgbF is a probable non-ribosomal peptide synthase proposed to contribute to agrobactin NRPS assembly from the BGC0002474 cluster.	https://www.ncbi.nlm.nih.gov/nuccore/AB083344.2 https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html https://www.uniprot.org/uniprotkb/Q83VM5 https://www.ncbi.nlm.nih.gov/protein/BAC57933.1 reference https://www.ncbi.nlm.nih.gov/nuccore/AB083344.2 evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes NCBI GenBank AB083344.2 is the 7,390 bp Agrobacterium tumefaciens MAFF301001 ferric iron uptake system gene cluster and annotates agbF/BAC57933.1. reference https://mibig.secondarymetabolites.org/repository/BGC0002474.2/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes MIBiG BGC0002474.2 lists agrobactin as the product of the Agrobacterium tumefaciens AB083344.2 cluster and annotates agbF/BAC57933.1 in that cluster. reference https://www.uniprot.org/uniprotkb/Q83VM5 evidence type DATABASE_ASSERTION snippet DR EMBL; AB083344; BAC57933.1; -; Genomic_DNA. retrieved on 2026-09-28 notes Unreviewed UniProtKB:Q83VM5 is Agrobacterium tumefaciens AgbF, length 548 aa, and cross-references EMBL AB083344 protein BAC57933.1. reference https://www.ncbi.nlm.nih.gov/protein/BAC57933.1 evidence type DATABASE_ASSERTION snippet probable non-ribosomal peptide synthase retrieved on 2026-09-28 notes NCBI GenPept BAC57933.1 is the AB083344.2:complement(104..1750) AgbF coding sequence from Agrobacterium tumefaciens strain MAFF301001.

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

Explore across X-Mech

AntibioticMech (agrobactin) ↗ MediaIngredientMech (naturalproductmech:mibig-bb581c6679) ↗ TaxonMech: Agrobacterium tumefaciens (NCBITaxon:358) ↗ PathwayMech (mibig:BGC0002474) ↗

Provenance

Source concept	Source	Version
BGC0002474	MIBIG	2

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