safracin B

naturalproductmech:mibig-592432a7ee 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	GKUZBRIJGIGFKC-ZWWMATSUSA-N
SMILES	CC1=C(OC)C(O)=C2[C@H]3[C@@H]4CC5=C(C(C(OC)=C(C)C5=O)=O)[C@H](CNC([C@@H](N)C)=O)N4C(O)[C@@H](CC2=C1)N3C
Stereochemistry	undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers

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
Pseudomonas fluorescens NCBITaxon:294	SOURCE_ASSERTION	mibig:BGC0000421	PMID:15773985

Occurrences 0

None cited.

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000421	Pseudomonas fluorescens NCBITaxon:294	CLUSTER_UNSTATED	genbank:AY061859.1

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.

Step	Enzyme	Reaction	Substrate → product	Evidence
1	SacF/SfcF C-methyltransferase UniProtKB:Q5JCL5	RHEA:41428	CHEBI:17895 + CHEBI:59789 → CHEBI:79076 + CHEBI:57856	DOI:10.1111/j.1365-2958.2004.04433.x

Step 1: MITE records SacF from BGC0000421 as the SAM-dependent C-methyltransferase that methylates L-tyrosine to 3-methyl-L-tyrosine, an intermediate toward the 3-hydroxy-5-methyl-O-methyltyrosine residues of safracin B.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 4 nodes, 3 edges

Pseudomonas fluorescens A2-2 SacF/SfcF C-methylates L-tyrosine with S-adenosyl-L-methionine to form 3-methyl-L-tyrosine during safracin B precursor biosynthesis.

Subject	Predicate	Object	Evidence
L-tyrosine	is C-methylated by	SacF/SfcF	DOI:10.1111/j.1365-2958.2004.04433.x https://mite.bioinformatics.nl/repository/MITE0000031 https://mibig.secondarymetabolites.org/repository/BGC0000421.5/BGC0000421.gbk https://www.uniprot.org/uniprotkb/Q5JCL5 https://www.ncbi.nlm.nih.gov/protein/AAL33761.1 https://www.rhea-db.org/rhea/41428 reference DOI:10.1111/j.1365-2958.2004.04433.x evidence type PRIMARY_EXPERIMENT snippet Cross-feeding experiments have confirmed that 3-hydroxy-5-methyl-O-methyltyrosine is the precursor of two amino acids of the molecule. notes Velasco et al. cloned and sequenced the Pseudomonas fluorescens A2-2 safracin cluster; MITE cites this paper for the SacF C-methylation entry with in vitro and knockout evidence. reference https://mite.bioinformatics.nl/repository/MITE0000031 evidence type DATABASE_ASSERTION retrieved on 2026-10-02 notes MITE0000031 is active and links SacF to UniProtKB:Q5JCL5, GenPept AAL33761.1, MIBiG BGC0000421, the Velasco et al. DOI, and the L-tyrosine to 3-methyl-L-tyrosine methylation reaction. reference https://mibig.secondarymetabolites.org/repository/BGC0000421.5/BGC0000421.gbk evidence type DATABASE_ASSERTION retrieved on 2026-10-02 notes MIBiG BGC0000421.5 places the Pseudomonas fluorescens A2-2 sfcF CDS at 14780..15847 with GenPept protein_id AAL33761.1 and a MITE0000031 100% identity gene-function annotation. reference https://www.uniprot.org/uniprotkb/Q5JCL5 evidence type DATABASE_ASSERTION retrieved on 2026-10-02 notes UniProtKB:Q5JCL5 resolves to the 355 aa Pseudomonas fluorescens sfcF putative methyltransferase from EMBL AY061859 / GenPept AAL33761.1 and cites DOI:10.1111/j.1365-2958.2004.04433.x. reference https://www.ncbi.nlm.nih.gov/protein/AAL33761.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-02 notes NCBI Protein AAL33761.1 is the Pseudomonas fluorescens A2-2 sfcF putative methyltransferase translated from AY061859.1:14780..15847. reference https://www.rhea-db.org/rhea/41428 evidence type DATABASE_ASSERTION retrieved on 2026-10-02 notes RHEA:41428 represents L-tyrosine plus S-adenosyl-L-methionine yielding 3-methyl-L-tyrosine, S-adenosyl-L-homocysteine and H(+).
S-adenosyl-L-methionine	is used by	SacF/SfcF	DOI:10.1111/j.1365-2958.2004.04433.x https://mite.bioinformatics.nl/repository/MITE0000031 https://mibig.secondarymetabolites.org/repository/BGC0000421.5/BGC0000421.gbk https://www.uniprot.org/uniprotkb/Q5JCL5 https://www.ncbi.nlm.nih.gov/protein/AAL33761.1 https://www.rhea-db.org/rhea/41428 reference DOI:10.1111/j.1365-2958.2004.04433.x evidence type PRIMARY_EXPERIMENT snippet Cross-feeding experiments have confirmed that 3-hydroxy-5-methyl-O-methyltyrosine is the precursor of two amino acids of the molecule. notes Velasco et al. cloned and sequenced the Pseudomonas fluorescens A2-2 safracin cluster; MITE cites this paper for the SacF C-methylation entry with in vitro and knockout evidence. reference https://mite.bioinformatics.nl/repository/MITE0000031 evidence type DATABASE_ASSERTION retrieved on 2026-10-02 notes MITE0000031 is active and links SacF to UniProtKB:Q5JCL5, GenPept AAL33761.1, MIBiG BGC0000421, the Velasco et al. DOI, and the L-tyrosine to 3-methyl-L-tyrosine methylation reaction. reference https://mibig.secondarymetabolites.org/repository/BGC0000421.5/BGC0000421.gbk evidence type DATABASE_ASSERTION retrieved on 2026-10-02 notes MIBiG BGC0000421.5 places the Pseudomonas fluorescens A2-2 sfcF CDS at 14780..15847 with GenPept protein_id AAL33761.1 and a MITE0000031 100% identity gene-function annotation. reference https://www.uniprot.org/uniprotkb/Q5JCL5 evidence type DATABASE_ASSERTION retrieved on 2026-10-02 notes UniProtKB:Q5JCL5 resolves to the 355 aa Pseudomonas fluorescens sfcF putative methyltransferase from EMBL AY061859 / GenPept AAL33761.1 and cites DOI:10.1111/j.1365-2958.2004.04433.x. reference https://www.ncbi.nlm.nih.gov/protein/AAL33761.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-02 notes NCBI Protein AAL33761.1 is the Pseudomonas fluorescens A2-2 sfcF putative methyltransferase translated from AY061859.1:14780..15847. reference https://www.rhea-db.org/rhea/41428 evidence type DATABASE_ASSERTION retrieved on 2026-10-02 notes RHEA:41428 represents L-tyrosine plus S-adenosyl-L-methionine yielding 3-methyl-L-tyrosine, S-adenosyl-L-homocysteine and H(+).
SacF/SfcF	forms	3-methyl-L-tyrosine	DOI:10.1111/j.1365-2958.2004.04433.x https://mite.bioinformatics.nl/repository/MITE0000031 https://mibig.secondarymetabolites.org/repository/BGC0000421.5/BGC0000421.gbk https://www.uniprot.org/uniprotkb/Q5JCL5 https://www.ncbi.nlm.nih.gov/protein/AAL33761.1 https://www.rhea-db.org/rhea/41428 reference DOI:10.1111/j.1365-2958.2004.04433.x evidence type PRIMARY_EXPERIMENT snippet Cross-feeding experiments have confirmed that 3-hydroxy-5-methyl-O-methyltyrosine is the precursor of two amino acids of the molecule. notes Velasco et al. cloned and sequenced the Pseudomonas fluorescens A2-2 safracin cluster; MITE cites this paper for the SacF C-methylation entry with in vitro and knockout evidence. reference https://mite.bioinformatics.nl/repository/MITE0000031 evidence type DATABASE_ASSERTION retrieved on 2026-10-02 notes MITE0000031 is active and links SacF to UniProtKB:Q5JCL5, GenPept AAL33761.1, MIBiG BGC0000421, the Velasco et al. DOI, and the L-tyrosine to 3-methyl-L-tyrosine methylation reaction. reference https://mibig.secondarymetabolites.org/repository/BGC0000421.5/BGC0000421.gbk evidence type DATABASE_ASSERTION retrieved on 2026-10-02 notes MIBiG BGC0000421.5 places the Pseudomonas fluorescens A2-2 sfcF CDS at 14780..15847 with GenPept protein_id AAL33761.1 and a MITE0000031 100% identity gene-function annotation. reference https://www.uniprot.org/uniprotkb/Q5JCL5 evidence type DATABASE_ASSERTION retrieved on 2026-10-02 notes UniProtKB:Q5JCL5 resolves to the 355 aa Pseudomonas fluorescens sfcF putative methyltransferase from EMBL AY061859 / GenPept AAL33761.1 and cites DOI:10.1111/j.1365-2958.2004.04433.x. reference https://www.ncbi.nlm.nih.gov/protein/AAL33761.1 evidence type DATABASE_ASSERTION retrieved on 2026-10-02 notes NCBI Protein AAL33761.1 is the Pseudomonas fluorescens A2-2 sfcF putative methyltransferase translated from AY061859.1:14780..15847. reference https://www.rhea-db.org/rhea/41428 evidence type DATABASE_ASSERTION retrieved on 2026-10-02 notes RHEA:41428 represents L-tyrosine plus S-adenosyl-L-methionine yielding 3-methyl-L-tyrosine, S-adenosyl-L-homocysteine and H(+).

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

Explore across X-Mech

AntibioticMech (safracin B) ↗ MediaIngredientMech (naturalproductmech:mibig-592432a7ee) ↗ TaxonMech: Pseudomonas fluorescens (NCBITaxon:294) ↗ PathwayMech (mibig:BGC0000421) ↗

Provenance

Source concept	Source	Version
BGC0000421	MIBIG	5

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