achromobactin free acid

CHEBI:65352 EXACT REVIEWED

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A tetracarboxylic acid obtained by protonation of the four carboxylate groups of achromobactin. A siderophore biosynthesized by prokaryotes.

Structure

Standard InChIKey	JIVPNYWQBCSFIL-MAVSXWESSA-N
SMILES	O=C(C[C@@](O)(CC(=O)OCCN1C(=O)CCC1(O)C(=O)O)C(=O)O)NCCC(C(=O)O)N1C(=O)CCC1(O)C(=O)O
Stereochemistry	undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers

Filing pathway

Amino acids and peptides — computed by NPClassifier npclassifier.gnps2.org@2026-10-30, which is why it is pinned rather than recomputed.

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.

Taxon	Basis	Cluster	Evidence
Dickeya chrysanthemi Strain: 3937 NCBITaxon:556	BGC_CHARACTERIZED		PMID:15612933 reference PMID:15612933 evidence type PRIMARY_EXPERIMENT notes Genetic inactivation of the acsABCDEF biosynthetic operon and structural elucidation (PMID:10928541) establish biosynthesis of achromobactin by Dickeya chrysanthemi 3937.
Pseudomonas syringae pv. syringae Strain: B728a NCBITaxon:321	BGC_CHARACTERIZED		PMID:19482931 reference PMID:19482931 evidence type PRIMARY_EXPERIMENT notes Targeted deletion and biochemical reconstitution of the acs biosynthetic gene cluster in Pseudomonas syringae pv. syringae B728a establish biosynthesis of achromobactin.

Occurrences 0

None cited.

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	AcsD (NIS synthetase) and AcsE (decarboxylase)		CHEBI:30769 + CHEBI:17115 → ungrounded	PMID:19182782
2	AcsA and AcsC (NIS siderophore synthetases)		CHEBI:30915 → CHEBI:65352	PMID:19482931

Step 1: ATP-dependent enantioselective condensation of citric acid with L-serine by AcsD followed by PLP-dependent decarboxylation by AcsE to O-citryl-ethanolamine.

Step 2: Amide condensation of O-citryl-ethanolamine with L-2,4-diaminobutyrate and two equivalents of 2-oxoglutaric acid to install the two 4-carboxy-4-oxobutanoyl chelating arms of achromobactin.

Mechanism & Biosynthesis Overview

Causal graph — bioactivity 8 nodes, 7 edges

NIS-mediated biosynthesis of the citrate/2-oxoglutarate polycarboxylate siderophore achromobactin by the acsABCDEF operon in Dickeya dadantii and Pseudomonas syringae and chelation of Fe(III) and CMM cations Ga(III) and La(III).

Subject	Predicate	Object	Notes	Evidence
citric acid	substrate_of	acsABCDEF biosynthetic operon	Citric acid forms the central alpha-hydroxycarboxylate core of achromobactin.	PMID:19182782 reference PMID:19182782 evidence type PRIMARY_EXPERIMENT notes AcsD activates a prochiral carboxymethyl group of citric acid for esterification with L-serine.
L-serine	substrate_of	acsABCDEF biosynthetic operon	L-serine is esterified onto citrate and decarboxylated to an ethanolamine linker.	PMID:19482931 reference PMID:19482931 evidence type PRIMARY_EXPERIMENT notes L-serine is condensed onto citrate by AcsD and decarboxylated by AcsE.
acsABCDEF biosynthetic operon	synthesizes	achromobactin free acid	acsABCDEF enzymes assemble achromobactin free acid.	PMID:15612933 reference PMID:15612933 evidence type PRIMARY_EXPERIMENT notes The acsABCDEF operon directs achromobactin biosynthesis in Dickeya dadantii 3937.
achromobactin free acid	chelates	iron(3+)	Coordinates Fe(III) via alpha-hydroxycarboxylate and alpha-keto/carboxylate oxygen donors.	PMID:10928541 reference PMID:10928541 evidence type PRIMARY_EXPERIMENT notes Achromobactin chelates ferric iron via its citrate and alpha-ketoglutarate carboxylate groups.
iron(3+)	enables	siderophore transport	Imported via the outer-membrane receptor Acr and CbrABCD ABC permease.	PMID:15612933 reference PMID:15612933 evidence type PRIMARY_EXPERIMENT notes Ferric-achromobactin is transported into Dickeya dadantii cells to support growth under iron depletion.
achromobactin free acid	chelates	gallium(3+)	[CMM] In vitro coordination of trivalent gallium(3+) by the polycarboxylate oxygen donor set.	PMID:10928541 reference PMID:10928541 evidence type PRIMARY_EXPERIMENT notes Trivalent metal binding by the citrate/alpha-ketoglutarate donor groups of achromobactin.
achromobactin free acid	chelates	lanthanum(3+)	[CMM] In vitro coordination of trivalent rare earth lanthanum(3+) by the pentacarboxylate scaffold.	PMID:38004684 reference PMID:38004684 evidence type PRIMARY_EXPERIMENT notes Bacterial metallophore chelation of rare earth elements including La(III).

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

Molecular targets 3

Target	Target organism	Measurement	Evidence
iron(3+) OTHER BINDS Primary physiological ferric ion chelation via alpha-hydroxycarboxylate and polycarboxylate coordination (citrate + 2-oxoglutarate-derived scaffold).			PMID:10928541 PMID:15612933 PMID:19482931 reference PMID:10928541 evidence type PRIMARY_EXPERIMENT notes Isolation and structural elucidation of the citrate polycarboxylate siderophore achromobactin and its ferric complex from Erwinia chrysanthemi. reference PMID:15612933 evidence type PRIMARY_EXPERIMENT notes The acsABCDEF operon of Erwinia chrysanthemi (Dickeya dadantii) 3937 directs biosynthesis of achromobactin required for ferric iron transport and plant infection. reference PMID:19482931 evidence type PRIMARY_EXPERIMENT notes Enzymatic reconstitution of achromobactin biosynthesis from citric acid, L-serine, 2,4-diaminobutyrate, and 2-oxoglutarate in Pseudomonas syringae pv. syringae B728a.
gallium(3+) OTHER BINDS [Critical Mineral & Material (CMM)] Coordination of trivalent gallium(3+) in vitro via the central citrate alpha-hydroxycarboxylate and flanking alpha-keto/carboxylate donor groups (redox-stable trivalent Fe(III) analog).			PMID:10928541 reference PMID:10928541 evidence type PRIMARY_EXPERIMENT notes Characterization of the polycarboxylate/alpha-hydroxycarboxylate trivalent metal-chelating scaffold of achromobactin.
lanthanum(3+) OTHER BINDS [Critical Mineral & Material (CMM)] In vitro polycarboxylate coordination of trivalent rare earth element lanthanum(3+) via the five carboxylate and alpha-hydroxy/keto oxygen donor atoms of achromobactin (hard oxygen-donor affinity; non-physiological in Dickeya/Pseudomonas).			PMID:38004684 reference PMID:38004684 evidence type PRIMARY_EXPERIMENT notes Bacterial polycarboxylate/hydroxamate metallophore chelation activity toward rare earth elements including La(III).

Explore across X-Mech

AntibioticMech (achromobactin free acid) ↗ MediaIngredientMech (CHEBI:65352) ↗ TaxonMech: Dickeya chrysanthemi (NCBITaxon:556) ↗ TaxonMech: Pseudomonas syringae pv. syringae (NCBITaxon:321) ↗

Provenance

Source concept	Source	Version
CHEBI:65352	CHEBI	3-star

This page is generated from data/natural_products/amino_acids_and_peptides/achromobactin-free-acid.yaml, which is generated from the committed inventories. Neither is edited by hand.