staphyloferrin A

CHEBI:84711 EXACT SEEDED

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 D-ornithine derivative obtained by formal condensation of the terminal carboxy groups of two citric acid units with the two amino groups of D-ornithine.

Structure

Standard InChIKey	VJSIXUQLTJCRCS-PJPOUAMNSA-N
SMILES	O=C(O)[C@H](NC(CC(C(O)=O)(O)CC(O)=O)=O)CCCNC(CC(C(O)=O)(O)CC(O)=O)=O
Stereochemistry	undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers

Filing pathway

Unclassified — 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
Staphylococcus aureus subsp. aureus NCTC 8325 NCBITaxon:93061	BGC_CHARACTERIZED	mibig:BGC0000944	PMID:19138128

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
Staphylococcus hyicus NCBITaxon:1284	CHEBI	PMID:2379505

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000944	Staphylococcus aureus subsp. aureus NCTC 8325 NCBITaxon:93061	CLUSTER_DEMONSTRATED	genbank:CP000253.1

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.

#	Enzyme	Reaction	Substrate → product	Evidence
1	SfnaD (NCTC 8325 reference) UniProtKB:Q2FW70	RHEA:59136	CHEBI:57668 + CHEBI:16947 → CHEBI:142972	https://www.uniprot.org/uniprotkb/Q2FW70
2	Staphyloferrin A synthase UniProtKB:Q2FW72	RHEA:59140	CHEBI:142972 + CHEBI:16947 → CHEBI:84711	DOI:10.1021/bi801844c

Entry 1: ATP-dependent condensation of D-ornithine and citrate forms the N(5)-citryl-D-ornithine intermediate, AMP, diphosphate and a proton. Database-qualified assignment to the NCTC 8325 reference; the UniProt publication block names RN4220, not an experimentally established identical stock. No step number is invented. This intermediate feeds the separately preserved terminal SfnaB step 3; existing numbering and primary evidence are unchanged. No L-ornithine racemase assignment to Q2FW73 is made.

Entry 2: Staphylococcus aureus NCTC 8325 SfnaB catalyzes the ATP-dependent terminal condensation of the SfnaD product with citrate to form staphyloferrin A. RHEA:59140 uses the stereospecified anionic staphyloferrin A participant CHEBI:142973; this record denotes neutral CHEBI:84711, whose seeded MIBiG structure leaves the citryl stereocentres unspecified.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 4 nodes, 3 edges

Staphylococcus aureus NCTC 8325 SfnaB-catalyzed terminal condensation of citrate with the SfnaD product in staphyloferrin A biosynthesis.

Subject	Predicate	Object	Notes	Evidence
N(5)-[(S)-citryl]-D-ornithine	is condensed with citrate by	SfnaB	RHEA:59140 represents this acceptor as CHEBI:142972, the N(5)-citryl-D-ornithine product of the preceding SfnaD synthetase reaction.	DOI:10.1021/bi801844c https://mibig.secondarymetabolites.org/repository/BGC0000944.5/ RHEA:59140 https://www.uniprot.org/uniprotkb/Q2FW72 reference DOI:10.1021/bi801844c evidence type PRIMARY_EXPERIMENT snippet SfnaB utilizing the alpha-amine to complete staphyloferrin A synthesis notes Cotton et al. reconstituted staphyloferrin A biosynthesis in vitro with purified recombinant SfnaD and SfnaB and assigned SfnaB as the final NIS synthetase that condenses citrate with the SfnaD product. reference https://mibig.secondarymetabolites.org/repository/BGC0000944.5/ evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes MIBiG entry version 5 links BGC0000944 to staphyloferrin A biosynthesis in Staphylococcus aureus subsp. aureus NCTC 8325. reference RHEA:59140 evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes RHEA:59140 annotates EC:6.3.2.57 as N(5)-[(S)-citryl]-D-ornithine, citrate, and ATP forming staphyloferrin A, AMP, diphosphate, and a proton. reference https://www.uniprot.org/uniprotkb/Q2FW72 evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes Reviewed UniProtKB:Q2FW72 is the Staphylococcus aureus NCTC 8325 / PS 47 SfnaB staphyloferrin A synthase, ordered locus SAOUHSC_02434, and annotates RHEA:59140.
citrate	is ligated to N(5)-citryl-D-ornithine by	SfnaB	RHEA:59140 consumes ATP and releases AMP, diphosphate, and a proton.	DOI:10.1021/bi801844c https://mibig.secondarymetabolites.org/repository/BGC0000944.5/ RHEA:59140 https://www.uniprot.org/uniprotkb/Q2FW72 reference DOI:10.1021/bi801844c evidence type PRIMARY_EXPERIMENT snippet SfnaB utilizing the alpha-amine to complete staphyloferrin A synthesis notes Cotton et al. reconstituted staphyloferrin A biosynthesis in vitro with purified recombinant SfnaD and SfnaB and assigned SfnaB as the final NIS synthetase that condenses citrate with the SfnaD product. reference https://mibig.secondarymetabolites.org/repository/BGC0000944.5/ evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes MIBiG entry version 5 links BGC0000944 to staphyloferrin A biosynthesis in Staphylococcus aureus subsp. aureus NCTC 8325. reference RHEA:59140 evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes RHEA:59140 annotates EC:6.3.2.57 as N(5)-[(S)-citryl]-D-ornithine, citrate, and ATP forming staphyloferrin A, AMP, diphosphate, and a proton. reference https://www.uniprot.org/uniprotkb/Q2FW72 evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes Reviewed UniProtKB:Q2FW72 is the Staphylococcus aureus NCTC 8325 / PS 47 SfnaB staphyloferrin A synthase, ordered locus SAOUHSC_02434, and annotates RHEA:59140.
SfnaB	forms	staphyloferrin A	RHEA uses stereospecified anionic staphyloferrin A CHEBI:142973 as the product participant; this graph points at neutral CHEBI:84711, the exact structure recorded for BGC0000944.	DOI:10.1021/bi801844c https://mibig.secondarymetabolites.org/repository/BGC0000944.5/ RHEA:59140 https://www.uniprot.org/uniprotkb/Q2FW72 reference DOI:10.1021/bi801844c evidence type PRIMARY_EXPERIMENT snippet SfnaB utilizing the alpha-amine to complete staphyloferrin A synthesis notes Cotton et al. reconstituted staphyloferrin A biosynthesis in vitro with purified recombinant SfnaD and SfnaB and assigned SfnaB as the final NIS synthetase that condenses citrate with the SfnaD product. reference https://mibig.secondarymetabolites.org/repository/BGC0000944.5/ evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes MIBiG entry version 5 links BGC0000944 to staphyloferrin A biosynthesis in Staphylococcus aureus subsp. aureus NCTC 8325. reference RHEA:59140 evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes RHEA:59140 annotates EC:6.3.2.57 as N(5)-[(S)-citryl]-D-ornithine, citrate, and ATP forming staphyloferrin A, AMP, diphosphate, and a proton. reference https://www.uniprot.org/uniprotkb/Q2FW72 evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes Reviewed UniProtKB:Q2FW72 is the Staphylococcus aureus NCTC 8325 / PS 47 SfnaB staphyloferrin A synthase, ordered locus SAOUHSC_02434, and annotates RHEA:59140.

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

Causal graph — biosynthesis 4 nodes, 3 edges

Database-qualified SfnaD condensation of D-ornithine and citrate in the NCTC 8325 reference. The CHEBI:142972 intermediate feeds the separately retained SfnaB graph; all edges here are graph-local. RN4220 assay annotation is not reference-stock identity. No precursor racemase function or final-product stereochemical completion is asserted. Conflicting MIBiG gene assignments are documented, not adopted.

Subject	Predicate	Object	Notes	Evidence
D-ornithinium(1+)	is a substrate for	SfnaD (SAOUHSC_02436; NCTC 8325 reference)	ATP-dependent condensation of D-ornithine and citrate forms the N(5)-citryl-D-ornithine intermediate, AMP, diphosphate and a proton.	https://www.uniprot.org/uniprotkb/Q2FW70 https://www.ncbi.nlm.nih.gov/protein/ABD31458.1 https://mibig.secondarymetabolites.org/repository/BGC0000944.5/annotations.json reference https://www.uniprot.org/uniprotkb/Q2FW70 evidence type DATABASE_ASSERTION retrieved on 2026-10-09 notes Reviewed UniProt entry version 93, sequence version 1; 658 aa; sfnaD, SAOUHSC_02436; S. aureus NCTC 8325 / PS 47, taxon 93061. ATP-dependent condensation of D-ornithine and citrate forms the N(5)-citryl-D-ornithine intermediate, AMP, diphosphate and a proton. FUNCTION and CATALYTIC ACTIVITY cite ECO:0000269/PMID:19138128. Its UniProt reference block names strain RN4220, not the NCTC 8325 reference stock. DOI:10.1021/bi801844c was tool-inaccessible in this audit; no new PRIMARY_EXPERIMENT claim or assayed-construct identity. RHEA:59136 and forward RHEA:59137 are read from UniProt, not independently rechecked against Rhea. Ionic participants follow UniProt cross-references and cached ChEBI release 255 labels; edges summarize principal substrates/products, not a complete stoichiometric model. snippet Catalyzes the ATP-dependent condensation of D-ornithine and citrate to form a citryl-D-ornithine intermediate reference https://www.ncbi.nlm.nih.gov/protein/ABD31458.1 evidence type CURATOR_INFERENCE retrieved on 2026-10-09 notes The complete 658-aa ABD31458.1 equals canonical UniProt Q2FW70. CDS CP000253.1:2262005..2263981, locus SAOUHSC_02436, independently translates to that sequence using table 11 and codon_start 1, with the recorded strand. CP000253.1 and GenPept name NCTC 8325, taxon 93061, BioSample SAMN02604235. This is reference identity only, not RN4220 equivalence, a historical stock, an assayed construct, native expression or functional proof. Genomic hypothetical-protein annotations are not functional experiments. reference https://mibig.secondarymetabolites.org/repository/BGC0000944.5/annotations.json evidence type DATABASE_ASSERTION retrieved on 2026-10-09 notes Source conflict, not functional support: MIBiG version 5 assigns SAOUHSC_02436 as sfaC (ornithine racemase), whereas the inspected UniProt entry Q2FW70 assigns sfnaD and the condensation reaction to this exact reference sequence. The conflicting MIBiG gene name/function is not adopted. Genomic coordinates ground reference identity; UniProt supplies the qualified function. No raw source correction or producer/locus evidence-grade change is made.
citrate(3-)	is a substrate for	SfnaD (SAOUHSC_02436; NCTC 8325 reference)	ATP-dependent condensation of D-ornithine and citrate forms the N(5)-citryl-D-ornithine intermediate, AMP, diphosphate and a proton.	https://www.uniprot.org/uniprotkb/Q2FW70 https://www.ncbi.nlm.nih.gov/protein/ABD31458.1 https://mibig.secondarymetabolites.org/repository/BGC0000944.5/annotations.json reference https://www.uniprot.org/uniprotkb/Q2FW70 evidence type DATABASE_ASSERTION retrieved on 2026-10-09 notes Reviewed UniProt entry version 93, sequence version 1; 658 aa; sfnaD, SAOUHSC_02436; S. aureus NCTC 8325 / PS 47, taxon 93061. ATP-dependent condensation of D-ornithine and citrate forms the N(5)-citryl-D-ornithine intermediate, AMP, diphosphate and a proton. FUNCTION and CATALYTIC ACTIVITY cite ECO:0000269/PMID:19138128. Its UniProt reference block names strain RN4220, not the NCTC 8325 reference stock. DOI:10.1021/bi801844c was tool-inaccessible in this audit; no new PRIMARY_EXPERIMENT claim or assayed-construct identity. RHEA:59136 and forward RHEA:59137 are read from UniProt, not independently rechecked against Rhea. Ionic participants follow UniProt cross-references and cached ChEBI release 255 labels; edges summarize principal substrates/products, not a complete stoichiometric model. reference https://www.ncbi.nlm.nih.gov/protein/ABD31458.1 evidence type CURATOR_INFERENCE retrieved on 2026-10-09 notes The complete 658-aa ABD31458.1 equals canonical UniProt Q2FW70. CDS CP000253.1:2262005..2263981, locus SAOUHSC_02436, independently translates to that sequence using table 11 and codon_start 1, with the recorded strand. CP000253.1 and GenPept name NCTC 8325, taxon 93061, BioSample SAMN02604235. This is reference identity only, not RN4220 equivalence, a historical stock, an assayed construct, native expression or functional proof. Genomic hypothetical-protein annotations are not functional experiments. reference https://mibig.secondarymetabolites.org/repository/BGC0000944.5/annotations.json evidence type DATABASE_ASSERTION retrieved on 2026-10-09 notes Source conflict, not functional support: MIBiG version 5 assigns SAOUHSC_02436 as sfaC (ornithine racemase), whereas the inspected UniProt entry Q2FW70 assigns sfnaD and the condensation reaction to this exact reference sequence. The conflicting MIBiG gene name/function is not adopted. Genomic coordinates ground reference identity; UniProt supplies the qualified function. No raw source correction or producer/locus evidence-grade change is made.
SfnaD (SAOUHSC_02436; NCTC 8325 reference)	forms	N(5)-[(S)-citryl]-D-ornithine(2-)	ATP-dependent condensation of D-ornithine and citrate forms the N(5)-citryl-D-ornithine intermediate, AMP, diphosphate and a proton.	https://www.uniprot.org/uniprotkb/Q2FW70 https://www.ncbi.nlm.nih.gov/protein/ABD31458.1 https://mibig.secondarymetabolites.org/repository/BGC0000944.5/annotations.json reference https://www.uniprot.org/uniprotkb/Q2FW70 evidence type DATABASE_ASSERTION retrieved on 2026-10-09 notes Reviewed UniProt entry version 93, sequence version 1; 658 aa; sfnaD, SAOUHSC_02436; S. aureus NCTC 8325 / PS 47, taxon 93061. ATP-dependent condensation of D-ornithine and citrate forms the N(5)-citryl-D-ornithine intermediate, AMP, diphosphate and a proton. FUNCTION and CATALYTIC ACTIVITY cite ECO:0000269/PMID:19138128. Its UniProt reference block names strain RN4220, not the NCTC 8325 reference stock. DOI:10.1021/bi801844c was tool-inaccessible in this audit; no new PRIMARY_EXPERIMENT claim or assayed-construct identity. RHEA:59136 and forward RHEA:59137 are read from UniProt, not independently rechecked against Rhea. Ionic participants follow UniProt cross-references and cached ChEBI release 255 labels; edges summarize principal substrates/products, not a complete stoichiometric model. reference https://www.ncbi.nlm.nih.gov/protein/ABD31458.1 evidence type CURATOR_INFERENCE retrieved on 2026-10-09 notes The complete 658-aa ABD31458.1 equals canonical UniProt Q2FW70. CDS CP000253.1:2262005..2263981, locus SAOUHSC_02436, independently translates to that sequence using table 11 and codon_start 1, with the recorded strand. CP000253.1 and GenPept name NCTC 8325, taxon 93061, BioSample SAMN02604235. This is reference identity only, not RN4220 equivalence, a historical stock, an assayed construct, native expression or functional proof. Genomic hypothetical-protein annotations are not functional experiments. reference https://mibig.secondarymetabolites.org/repository/BGC0000944.5/annotations.json evidence type DATABASE_ASSERTION retrieved on 2026-10-09 notes Source conflict, not functional support: MIBiG version 5 assigns SAOUHSC_02436 as sfaC (ornithine racemase), whereas the inspected UniProt entry Q2FW70 assigns sfnaD and the condensation reaction to this exact reference sequence. The conflicting MIBiG gene name/function is not adopted. Genomic coordinates ground reference identity; UniProt supplies the qualified function. No raw source correction or producer/locus evidence-grade change is made.

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

Causal graph — biosynthesis 2 nodes, 1 edge

Database-qualified involvement of SfaA in staphyloferrin A secretion, selecting the NCTC 8325 reference. The compound node is the neutral, partly stereounspecified owner anchor, not an established transported ionic species or fully specified stereoisomer.

Subject	Predicate	Object	Notes	Evidence
SfaA (SAOUHSC_02435; NCTC 8325 reference)	is involved in secretion of	staphyloferrin A	Secretion involvement only, not direct transport or essentiality. CHEBI:84711 is a compound anchor; no equivalence to stereospecified anionic CHEBI:142973, transported protonation state, or citryl-centre stereochemistry is established.	https://www.uniprot.org/uniprotkb/Q2FW71 https://www.ncbi.nlm.nih.gov/protein/ABD31457.1 https://mibig.secondarymetabolites.org/repository/BGC0000944.5/annotations.json reference https://www.uniprot.org/uniprotkb/Q2FW71 evidence type DATABASE_ASSERTION retrieved on 2026-10-09 notes Reviewed UniProt entry version 98, sequence version 1; 397 aa; sfaA, SAOUHSC_02435; S. aureus NCTC 8325 / PS 47, taxon 93061. FUNCTION cites ECO:0000269/PMID:25680529 for involvement in staphyloferrin A secretion. Protein existence remains 3 (inferred from homology), despite the reviewed entry and experimental-evidence annotation. DOI:10.1016/j.febslet.2015.02.002 was tool-inaccessible; no independently inspected primary experiment or assay-strain identity. No direct transport assay, essentiality, flux, substrate specificity, membrane topology, or staphyloferrin B secretion claim is adopted. snippet Involved in staphyloferrin A secretion reference https://www.ncbi.nlm.nih.gov/protein/ABD31457.1 evidence type CURATOR_INFERENCE retrieved on 2026-10-09 notes The complete 397-aa ABD31457.1 equals canonical UniProt Q2FW71. CDS complement(CP000253.1:2260710..2261903), locus SAOUHSC_02435, independently translates to that sequence using table 11 and codon_start 1, with the recorded strand. CP000253.1 and GenPept name NCTC 8325, taxon 93061, BioSample SAMN02604235. This is reference identity only, not RN4220 equivalence, a historical stock, an assayed construct, native expression or functional proof. Genomic hypothetical-protein annotations are not functional experiments. reference https://mibig.secondarymetabolites.org/repository/BGC0000944.5/annotations.json evidence type DATABASE_ASSERTION retrieved on 2026-10-09 notes Source conflict, not functional support: MIBiG version 5 assigns SAOUHSC_02435 as sfaB (NIS synthetase), whereas the inspected UniProt entry Q2FW71 assigns sfaA and secretion involvement to this exact reference sequence. The conflicting MIBiG gene name/function is not adopted. Genomic coordinates ground reference identity; UniProt supplies the qualified function. No raw source correction or producer/locus evidence-grade change is made.

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

Explore across X-Mech

AntibioticMech (staphyloferrin A) ↗ MediaIngredientMech (CHEBI:84711) ↗ TaxonMech: Staphylococcus aureus subsp. aureus NCTC 8325 (NCBITaxon:93061) ↗ PathwayMech (mibig:BGC0000944) ↗

Provenance

Source concept	Source	Version
BGC0000944	MIBIG	5
CHEBI:84711	CHEBI	3-star

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