rhodotorulic acid

CHEBI:84731 EXACT REVIEWED

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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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 member of the class of 2,5-diketopiperazines obtained by cyclodimerisation of N5-acetyl-N5-hydroxy-L-ornithine.

Structure

Standard InChIKey	PUWVNTVQJFSBDH-RYUDHWBXSA-N
SMILES	CC(=O)N(O)CCC[C@@H]1NC(=O)[C@H](CCCN(O)C(C)=O)NC1=O
Stereochemistry	fully defined

Filing pathway

Unclassified — computed by NPClassifier npclassifier.gnps2.org@2026-10-31, 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
Rhodotorula glutinis Strain: ATCC 26207 NCBITaxon:5535	AXENIC_CULTURE		PMID:4971459 reference PMID:4971459 evidence type PRIMARY_EXPERIMENT notes Isolation and structural elucidation of the diketopiperazine dihydroxamate siderophore rhodotorulic acid secreted in high yield by iron-deficient axenic cultures of Rhodotorula pilimanae (Rhodotorula glutinis ATCC 26207).
Rhodotorula mucilaginosa NCBITaxon:5537	AXENIC_CULTURE		PMID:14531617

Occurrences 1

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
Rhodotorula mucilaginosa NCBITaxon:5537	CHEBI	PMID:23490182

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	L-ornithine N5-monooxygenase		CHEBI:15729 → CHEBI:79095	PMID:4971459
2	N5-hydroxyornithine N5-acetyltransferase and rhodotorulic acid nonribosomal peptide synthetase (diketopiperazine cyclase)		CHEBI:79095 + CHEBI:15351 + CHEBI:15422 → CHEBI:84731	PMID:4971459

Step 1: N5-hydroxylation of L-ornithine to generate N(5)-hydroxy-L-ornithine.

Step 2: Acetyl-CoA-dependent N5-acetylation of N(5)-hydroxy-L-ornithine followed by ATP-dependent NRPS activation and head-to-tail cyclodimerization of two N5-acetyl-N5-hydroxy-L-ornithine units to form the 2,5-diketopiperazine dihydroxamate siderophore rhodotorulic acid.

Mechanism & Biosynthesis Overview

Causal graph — bioactivity 11 nodes, 10 edges

Biosynthesis of the diketopiperazine dihydroxamate siderophore rhodotorulic acid in basidiomycetous yeasts (Rhodotorula spp.), formation of binuclear 3:2 complexes with Fe(III) and CMM trivalent cations Ga(III), Al(III), and Cr(III), and bacterial xenosiderophore uptake via Escherichia coli FhuE.

Subject	Predicate	Object	Notes	Evidence
L-ornithine	converted_to	N(5)-hydroxy-L-ornithine	L-ornithine is N5-hydroxylated to N(5)-hydroxy-L-ornithine in the first committed step.	PMID:4971459 reference PMID:4971459 evidence type PRIMARY_EXPERIMENT notes Rhodotorulic acid is derived from L-ornithine via N(5)-hydroxy-L-ornithine.
acetyl-CoA	substrate_of	Rhodotorulic acid synthetase	Donates the N5-acetyl groups during N5-acetylation and diketopiperazine assembly.	PMID:4971459 reference PMID:4971459 evidence type PRIMARY_EXPERIMENT notes Each hydroxamate group carries an N-acetyl substituent.
N(5)-hydroxy-L-ornithine	substrate_of	Rhodotorulic acid synthetase	Two N(5)-hydroxy-L-ornithine units undergo N5-acetylation and head-to-tail condensation.	PMID:4971459 reference PMID:4971459 evidence type PRIMARY_EXPERIMENT notes Cyclodimerization forms the 2,5-diketopiperazine ring.
Rhodotorulic acid synthetase	synthesizes	rhodotorulic acid	Releases rhodotorulic acid.	PMID:14531617 reference PMID:14531617 evidence type PRIMARY_EXPERIMENT notes Iron-regulated production of rhodotorulic acid in Rhodotorula mucilaginosa.
rhodotorulic acid	chelates	iron(3+)	Forms the binuclear complex Fe2(RA)3 (log beta230 = 62.2).	PMID:11151360 reference PMID:11151360 evidence type PRIMARY_EXPERIMENT notes Thermodynamic and kinetic characterization of Fe2(RA)3.
rhodotorulic acid	chelates	gallium(3+)	[CMM] Coordinates trivalent gallium(3+) via reductive displacement of Fe(III).	PMID:2945591 reference PMID:2945591 evidence type PRIMARY_EXPERIMENT notes Quantitative displacement of Fe(III) by Ga(III) in ferric rhodotorulic acid.
rhodotorulic acid	chelates	aluminium(3+)	[CMM] Chelates and solubilizes trivalent aluminium(3+) in vitro.	PMID:2019981 reference PMID:2019981 evidence type PRIMARY_EXPERIMENT notes Aluminium solubilization and mobilization from transferrin by rhodotorulic acid.
rhodotorulic acid	chelates	chromium(3+)	[CMM] Forms kinetically inert binuclear Cr2(RA)3 complexes.	PMID:4055766 reference PMID:4055766 evidence type PRIMARY_EXPERIMENT notes Resolution and CD spectroscopy of delta and lambda isomers of Cr2(RA)3.
rhodotorulic acid	binds	Outer membrane receptor FhuE	In its ferric-complexed form Fe2(RA)3, rhodotorulic acid is recognized as a xenosiderophore by the E. coli outer membrane receptor FhuE.	PMID:6353165 reference PMID:6353165 evidence type PRIMARY_EXPERIMENT notes FhuE outer membrane receptor mediates ferric-rhodotorulate uptake in Escherichia coli K-12.
Outer membrane receptor FhuE	enables	iron ion transport	Translocates iron across the bacterial outer membrane.	PMID:6353165 reference PMID:6353165 evidence type PRIMARY_EXPERIMENT notes fhuE-dependent iron nutrition via rhodotorulic acid.

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

Molecular targets 4

Target	Target organism	Measurement	Evidence
iron(3+) OTHER BINDS Tetradentate dihydroxamate coordination of ferric iron(3+); because each rhodotorulic acid ligand provides only two hydroxamate donor groups (4 oxygen atoms), it forms a binuclear 3:2 ligand:metal complex Fe2(RA)3 at neutral pH (log beta230 = 62.2) that mediates ferric ion delivery to the cell surface in Rhodotorula.			PMID:4971459 PMID:30750 PMID:11151360 reference PMID:4971459 evidence type PRIMARY_EXPERIMENT notes Isolation, structural elucidation, and ferric complex stoichiometry (Fe2L3) of rhodotorulic acid from iron-deficient Rhodotorula pilimanae. reference PMID:30750 evidence type PRIMARY_EXPERIMENT notes Coordination chemistry and 55Fe uptake kinetics of ferric rhodotorulate in Rhodotorula pilimanae. reference PMID:11151360 evidence type PRIMARY_EXPERIMENT notes Spectrophotometric and stopped-flow kinetic characterization of proton-driven Fe(III) dissociation from the binuclear Fe2(rhodotorulate)3 complex in aqueous solution.
gallium(3+) OTHER BINDS [Critical Mineral & Material (CMM)] Coordination of trivalent gallium(3+) in aqueous solution; excess Ga(III) quantitatively and rapidly displaces Fe(III) from ferric rhodotorulic acid under reducing conditions (with maximal exchange rate at pH 6.5).			PMID:2945591 reference PMID:2945591 evidence type PRIMARY_EXPERIMENT notes Spectroscopic kinetic demonstration of quantitative reductive displacement of Fe(III) by Ga(III) in ferric rhodotorulic acid.
aluminium(3+) OTHER BINDS [Critical Mineral & Material (CMM)] Chelation of trivalent aluminium(3+) in vitro; rhodotorulic acid significantly solubilizes aluminium from insoluble aluminium borate and mobilizes Al(III) from human plasma transferrin.			PMID:2019981 reference PMID:2019981 evidence type PRIMARY_EXPERIMENT notes In vitro evaluation of rhodotorulic acid for aluminium(3+) solubilization, mobilization from transferrin, and octanol/aqueous complex partitioning.
chromium(3+) OTHER BINDS [Critical Mineral & Material (CMM)] Kinetically inert octahedral coordination of chromium(3+) in the binuclear complex Cr2(rhodotorulate)3 (resolved into delta-cis, delta-trans, and lambda-trans isomers) used to probe stereospecific cell-surface recognition in Rhodotorula pilimanae.			PMID:30750 PMID:4055766 reference PMID:30750 evidence type PRIMARY_EXPERIMENT notes Synthesis and transport study of kinetically inert chromic-substituted rhodotorulic acid complexes in Rhodotorula pilimanae. reference PMID:4055766 evidence type PRIMARY_EXPERIMENT notes Separation and visible/circular dichroism spectroscopic characterization of geometric and optical isomers of chromic rhodotorulate Cr2(RA)3.

Explore across X-Mech

AntibioticMech (rhodotorulic acid) ↗ MediaIngredientMech (CHEBI:84731) ↗ TaxonMech: Rhodotorula glutinis (NCBITaxon:5535) ↗ TaxonMech: Rhodotorula mucilaginosa (NCBITaxon:5537) ↗

Provenance

Source concept	Source	Version
CHEBI:84731	CHEBI	3-star

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