rhizobactin 1021

CHEBI:74252 EXACT REVIEWED

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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

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A hydoxy monocarboxylic acid that is citric acid in which the two carboxy groups attached to methylene groups have each been converted to the carboxamide arising by formal condensation with the primary amino group of N-hydroxypropane-1,3-diamine and in which the nitrogen of one of the hydroxylamino groups has been acetylated while the other has been acylated with a (2E)-dec-2-enoyl group. Rhizobactin 1021 is a siderophore obtained fromj the nitrogen-fixing alfalfa symbiont Rhizobium meliloti 1021.

Structure

Standard InChIKey	WRSKPFYPBJAAEG-FMIVXFBMSA-N
SMILES	CCCCCCC/C=C/C(=O)N(O)CCCNC(=O)CC(O)(CC(=O)NCCCN(O)C(C)=O)C(=O)O
Stereochemistry	undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers

Filing pathway

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

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
Sinorhizobium meliloti Strain: 2011 NCBITaxon:382	BGC_CHARACTERIZED		PMID:11274118 reference PMID:11274118 evidence type PRIMARY_EXPERIMENT notes Insertional mutagenesis and sequence characterization of the rhbABCDEF siderophore biosynthesis operon in Sinorhizobium meliloti establish biosynthesis of the asymmetric citrate-based dihydroxamate siderophore rhizobactin 1021.

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	RhbA (diaminobutyrate aminotransferase) and RhbB (diaminobutyrate decarboxylase)		ungrounded → ungrounded	PMID:11274118
2	RhbD (acyltransferase), RhbE (1,3-diaminopropane monooxygenase), RhbC and RhbF (NIS siderophore synthetases)		CHEBI:30769 + CHEBI:15351 → CHEBI:74252	PMID:11274118

Step 1: Condensation of L-aspartate 4-semialdehyde and L-glutamate to L-2,4-diaminobutyrate followed by pyridoxal 5'-phosphate-dependent decarboxylation to synthesize the symmetrical 1,3-diaminopropane diamine precursor in Sinorhizobium meliloti.

Step 2: N4-hydroxylation of 1,3-diaminopropane, asymmetric N-acylation with acetyl-CoA and (E)-dec-2-enoyl-ACP/CoA, and ATP-dependent NIS condensation with citric acid to yield rhizobactin 1021.

Mechanism & Biosynthesis Overview

Causal graph — bioactivity 7 nodes, 6 edges

NIS-mediated biosynthesis of the amphiphilic citrate-bishydroxamate siderophore rhizobactin 1021 by the rhbABCDEF operon in Sinorhizobium meliloti and hexadentate chelation of Fe(III) and CMM cation Ga(III).

Subject	Predicate	Object	Notes	Evidence
citric acid	substrate_of	rhbABCDEF biosynthetic operon	Citric acid provides the central alpha-hydroxycarboxylate backbone condensed by RhbC and RhbF.	PMID:11274118 reference PMID:11274118 evidence type PRIMARY_EXPERIMENT notes RhbC and RhbF are NIS synthetases that condense substituted 1,3-diaminopropane units onto citric acid.
acetyl-CoA	substrate_of	rhbABCDEF biosynthetic operon	Acetyl-CoA acylates one N-hydroxy-1,3-diaminopropane arm.	PMID:15990296 reference PMID:15990296 evidence type PRIMARY_EXPERIMENT notes Rhizobactin 1021 contains one N-acetyl-N-hydroxy-1,3-diaminopropane arm and one (E)-dec-2-enoyl arm.
rhbABCDEF biosynthetic operon	synthesizes	rhizobactin 1021	rhbABCDEF synthesizes rhizobactin 1021 in Sinorhizobium meliloti.	PMID:11274118 reference PMID:11274118 evidence type PRIMARY_EXPERIMENT notes Insertional mutagenesis in rhbABCDEF abolishes rhizobactin 1021 synthesis.
rhizobactin 1021	chelates	iron(3+)	Hexadentate coordination of Fe(III) via citrate alpha-hydroxycarboxylate and two hydroxamate groups.	PMID:15990296 reference PMID:15990296 evidence type PRIMARY_EXPERIMENT notes Rhizobactin 1021 forms a 1:1 hexadentate ferric complex.
iron(3+)	enables	siderophore transport	Ferric-rhizobactin 1021 is imported across the outer membrane by RhtA and across the inner membrane by RhtX.	PMID:15126460 reference PMID:15126460 evidence type PRIMARY_EXPERIMENT notes RhtX and RhtA mediate rhizobactin 1021 utilization in Sinorhizobium meliloti.
rhizobactin 1021	chelates	gallium(3+)	[CMM] In vitro hexadentate coordination of trivalent gallium(3+).	PMID:15990296 reference PMID:15990296 evidence type PRIMARY_EXPERIMENT notes Structural modeling of trivalent metal coordination by rhizobactin 1021.

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 hexadentate alpha-hydroxycarboxylate (citrate core) + bis-hydroxamate coordination (1:1 Fe(III)-rhizobactin 1021 complex).			PMID:11274118 PMID:15990296 reference PMID:11274118 evidence type PRIMARY_EXPERIMENT notes Genetic and functional characterization of the rhbABCDEF biosynthesis operon and rhtA outer-membrane receptor gene for the citrate-hydroxamate siderophore rhizobactin 1021 in Sinorhizobium meliloti 2011. reference PMID:15990296 evidence type PRIMARY_EXPERIMENT notes Total synthesis and structural modeling of the amphiphilic citrate-bishydroxamate siderophore rhizobactin 1021 and its Fe(III) complex.
gallium(3+) OTHER BINDS [Critical Mineral & Material (CMM)] Hexadentate coordination of trivalent gallium(3+) in vitro via the central citrate alpha-hydroxycarboxylate and two flanking N4-hydroxy-1,3-diaminopropane hydroxamate arms (diamagnetic Fe(III) surrogate).			PMID:15990296 reference PMID:15990296 evidence type PRIMARY_EXPERIMENT notes Structural characterization and metal coordination modeling of the hexadentate citrate-bishydroxamate scaffold of rhizobactin 1021.
copper(2+) OTHER BINDS In vitro coordination of divalent copper(2+) by the citrate-bishydroxamate scaffold of rhizobactin 1021 (secondary non-physiological complexation).			PMID:15990296 reference PMID:15990296 evidence type PRIMARY_EXPERIMENT notes Synthesis and coordination chemistry of the amphiphilic citrate-hydroxamate siderophore rhizobactin 1021.

Explore across X-Mech

AntibioticMech (rhizobactin 1021) ↗ MediaIngredientMech (CHEBI:74252) ↗ TaxonMech: Sinorhizobium meliloti (NCBITaxon:382) ↗

Provenance

Source concept	Source	Version
CHEBI:74252	CHEBI	3-star

This page is generated from data/natural_products/alkaloids/rhizobactin-1021.yaml, which is generated from the committed inventories. Neither is edited by hand.