saframycin A

naturalproductmech:mibig-5a2b2bf988 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	JNEGMBHBUAJRSX-SHUHUVMISA-N
SMILES	CC1=C(C(=O)C2=C(C1=O)C[C@H]3[C@H]4C5=C(C[C@H](N4C)[C@@H](N3[C@H]2CNC(=O)C(=O)C)C#N)C(=O)C(=C(C5=O)OC)C)OC
Stereochemistry	fully defined
Cross-references	pubchem:3086522, pubchem:100594

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
Streptomyces lavendulae NCBITaxon:1914	SOURCE_ASSERTION	mibig:BGC0000422	PMID:17981978

Occurrences 4

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
Streptomyces lavendulae NCBITaxon:1914	LOTUS	DOI:10.1128/AAC.28.1.5
Streptomyces lavendulae NCBITaxon:1914	LOTUS	DOI:10.1128/JB.00826-07
Streptomyces lavendulae NCBITaxon:1914	LOTUS	DOI:10.7164/ANTIBIOTICS.30.1015
Streptomyces lavendulae NCBITaxon:1914	LOTUS	DOI:10.7164/ANTIBIOTICS.41.734

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000422	Streptomyces lavendulae NCBITaxon:1914	CLUSTER_UNSTATED	genbank:DQ838002.1

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	SfmM2 L-tyrosine C(3)-methyltransferase UniProtKB:B0CN31	RHEA:41428	CHEBI:17895 + CHEBI:59789 → CHEBI:79076 + CHEBI:57856	DOI:10.1074/jbc.M111.306316

Step 1: SfmM2 catalyzes L-tyrosine C-methylation to 3-methyl-L-tyrosine, an intermediate toward the 3-hydroxy-5-methyl-O-methyltyrosine residue of saframycin A.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 4 nodes, 3 edges

Streptomyces lavendulae NRRL 11002 SfmM2 C-methylates L-tyrosine with S-adenosyl-L-methionine to form 3-methyl-L-tyrosine during saframycin A precursor biosynthesis.

Subject	Predicate	Object	Evidence
L-tyrosine	is C-methylated by	SfmM2	DOI:10.1074/jbc.M111.306316 DOI:10.1128/JB.00826-07 https://mite.bioinformatics.nl/repository/MITE0000032 https://mibig.secondarymetabolites.org/repository/BGC0000422.5/BGC0000422.gbk https://www.uniprot.org/uniprotkb/B0CN31 https://www.ncbi.nlm.nih.gov/protein/ABI22137.1 https://www.rhea-db.org/rhea/41428 reference DOI:10.1074/jbc.M111.306316 evidence type PRIMARY_EXPERIMENT snippet we elucidated the biosynthetic pathway of 3-OH-5-Me-OMe-Tyr by kinetic studies of SfmD in combination with biochemical assays of SfmM2, a methyltransferase within the same pathway notes Tang, Fu and Tang biochemically assayed SfmM2 while resolving the 3-hydroxy-5-methyl-O-methyltyrosine branch of saframycin A biosynthesis. reference DOI:10.1128/JB.00826-07 evidence type PRIMARY_EXPERIMENT snippet the biosynthetic gene cluster for SFM-A was cloned and localized to a 62-kb contiguous DNA region notes Li et al. cloned and sequenced the Streptomyces lavendulae NRRL 11002 saframycin A cluster, deposited DQ838002, and provided the genomic locus that encodes sfmM2. reference https://mite.bioinformatics.nl/repository/MITE0000032 evidence type DATABASE_ASSERTION retrieved on 2026-10-03 notes MITE0000032 is active, assigns SfmM2 to the C-methylation of L-tyrosine to 3-methyl-L-tyrosine, records RHEA:41428 and EC:2.1.1.304 for the reaction, and links SfmM2 to UniProtKB:B0CN31, GenPept ABI22137.1 and MIBiG BGC0000422. reference https://mibig.secondarymetabolites.org/repository/BGC0000422.5/BGC0000422.gbk evidence type DATABASE_ASSERTION snippet MITE0000032: Methylation (100% identity) retrieved on 2026-10-03 notes MIBiG BGC0000422.5 places the Streptomyces lavendulae NRRL 11002 sfmM2 CDS at DQ838002.1:41474..42574 with GenPept protein_id ABI22137.1 and a MITE0000032 100% identity methylation annotation. reference https://www.uniprot.org/uniprotkb/B0CN31 evidence type DATABASE_ASSERTION snippet GN Name=sfmM2 retrieved on 2026-10-03 notes Reviewed UniProtKB:B0CN31 resolves to the Streptomyces lavendulae L-tyrosine C(3)-methyltransferase SfmM2 entry, cross-references EMBL DQ838002 protein ABI22137.1, and annotates the RHEA:41428 / EC:2.1.1.304 catalytic activity. reference https://www.ncbi.nlm.nih.gov/protein/ABI22137.1 evidence type DATABASE_ASSERTION snippet /gene="sfmM2" retrieved on 2026-10-03 notes NCBI Protein ABI22137.1 is the 366 aa Streptomyces lavendulae NRRL 11002 SfmM2 protein translated from DQ838002.1:41474..42574. reference https://www.rhea-db.org/rhea/41428 evidence type DATABASE_ASSERTION retrieved on 2026-10-03 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	SfmM2	DOI:10.1074/jbc.M111.306316 DOI:10.1128/JB.00826-07 https://mite.bioinformatics.nl/repository/MITE0000032 https://mibig.secondarymetabolites.org/repository/BGC0000422.5/BGC0000422.gbk https://www.uniprot.org/uniprotkb/B0CN31 https://www.ncbi.nlm.nih.gov/protein/ABI22137.1 https://www.rhea-db.org/rhea/41428 reference DOI:10.1074/jbc.M111.306316 evidence type PRIMARY_EXPERIMENT snippet we elucidated the biosynthetic pathway of 3-OH-5-Me-OMe-Tyr by kinetic studies of SfmD in combination with biochemical assays of SfmM2, a methyltransferase within the same pathway notes Tang, Fu and Tang biochemically assayed SfmM2 while resolving the 3-hydroxy-5-methyl-O-methyltyrosine branch of saframycin A biosynthesis. reference DOI:10.1128/JB.00826-07 evidence type PRIMARY_EXPERIMENT snippet the biosynthetic gene cluster for SFM-A was cloned and localized to a 62-kb contiguous DNA region notes Li et al. cloned and sequenced the Streptomyces lavendulae NRRL 11002 saframycin A cluster, deposited DQ838002, and provided the genomic locus that encodes sfmM2. reference https://mite.bioinformatics.nl/repository/MITE0000032 evidence type DATABASE_ASSERTION retrieved on 2026-10-03 notes MITE0000032 is active, assigns SfmM2 to the C-methylation of L-tyrosine to 3-methyl-L-tyrosine, records RHEA:41428 and EC:2.1.1.304 for the reaction, and links SfmM2 to UniProtKB:B0CN31, GenPept ABI22137.1 and MIBiG BGC0000422. reference https://mibig.secondarymetabolites.org/repository/BGC0000422.5/BGC0000422.gbk evidence type DATABASE_ASSERTION snippet MITE0000032: Methylation (100% identity) retrieved on 2026-10-03 notes MIBiG BGC0000422.5 places the Streptomyces lavendulae NRRL 11002 sfmM2 CDS at DQ838002.1:41474..42574 with GenPept protein_id ABI22137.1 and a MITE0000032 100% identity methylation annotation. reference https://www.uniprot.org/uniprotkb/B0CN31 evidence type DATABASE_ASSERTION snippet GN Name=sfmM2 retrieved on 2026-10-03 notes Reviewed UniProtKB:B0CN31 resolves to the Streptomyces lavendulae L-tyrosine C(3)-methyltransferase SfmM2 entry, cross-references EMBL DQ838002 protein ABI22137.1, and annotates the RHEA:41428 / EC:2.1.1.304 catalytic activity. reference https://www.ncbi.nlm.nih.gov/protein/ABI22137.1 evidence type DATABASE_ASSERTION snippet /gene="sfmM2" retrieved on 2026-10-03 notes NCBI Protein ABI22137.1 is the 366 aa Streptomyces lavendulae NRRL 11002 SfmM2 protein translated from DQ838002.1:41474..42574. reference https://www.rhea-db.org/rhea/41428 evidence type DATABASE_ASSERTION retrieved on 2026-10-03 notes RHEA:41428 represents L-tyrosine plus S-adenosyl-L-methionine yielding 3-methyl-L-tyrosine, S-adenosyl-L-homocysteine and H(+).
SfmM2	forms	3-methyl-L-tyrosine	DOI:10.1074/jbc.M111.306316 DOI:10.1128/JB.00826-07 https://mite.bioinformatics.nl/repository/MITE0000032 https://mibig.secondarymetabolites.org/repository/BGC0000422.5/BGC0000422.gbk https://www.uniprot.org/uniprotkb/B0CN31 https://www.ncbi.nlm.nih.gov/protein/ABI22137.1 https://www.rhea-db.org/rhea/41428 reference DOI:10.1074/jbc.M111.306316 evidence type PRIMARY_EXPERIMENT snippet we elucidated the biosynthetic pathway of 3-OH-5-Me-OMe-Tyr by kinetic studies of SfmD in combination with biochemical assays of SfmM2, a methyltransferase within the same pathway notes Tang, Fu and Tang biochemically assayed SfmM2 while resolving the 3-hydroxy-5-methyl-O-methyltyrosine branch of saframycin A biosynthesis. reference DOI:10.1128/JB.00826-07 evidence type PRIMARY_EXPERIMENT snippet the biosynthetic gene cluster for SFM-A was cloned and localized to a 62-kb contiguous DNA region notes Li et al. cloned and sequenced the Streptomyces lavendulae NRRL 11002 saframycin A cluster, deposited DQ838002, and provided the genomic locus that encodes sfmM2. reference https://mite.bioinformatics.nl/repository/MITE0000032 evidence type DATABASE_ASSERTION retrieved on 2026-10-03 notes MITE0000032 is active, assigns SfmM2 to the C-methylation of L-tyrosine to 3-methyl-L-tyrosine, records RHEA:41428 and EC:2.1.1.304 for the reaction, and links SfmM2 to UniProtKB:B0CN31, GenPept ABI22137.1 and MIBiG BGC0000422. reference https://mibig.secondarymetabolites.org/repository/BGC0000422.5/BGC0000422.gbk evidence type DATABASE_ASSERTION snippet MITE0000032: Methylation (100% identity) retrieved on 2026-10-03 notes MIBiG BGC0000422.5 places the Streptomyces lavendulae NRRL 11002 sfmM2 CDS at DQ838002.1:41474..42574 with GenPept protein_id ABI22137.1 and a MITE0000032 100% identity methylation annotation. reference https://www.uniprot.org/uniprotkb/B0CN31 evidence type DATABASE_ASSERTION snippet GN Name=sfmM2 retrieved on 2026-10-03 notes Reviewed UniProtKB:B0CN31 resolves to the Streptomyces lavendulae L-tyrosine C(3)-methyltransferase SfmM2 entry, cross-references EMBL DQ838002 protein ABI22137.1, and annotates the RHEA:41428 / EC:2.1.1.304 catalytic activity. reference https://www.ncbi.nlm.nih.gov/protein/ABI22137.1 evidence type DATABASE_ASSERTION snippet /gene="sfmM2" retrieved on 2026-10-03 notes NCBI Protein ABI22137.1 is the 366 aa Streptomyces lavendulae NRRL 11002 SfmM2 protein translated from DQ838002.1:41474..42574. reference https://www.rhea-db.org/rhea/41428 evidence type DATABASE_ASSERTION retrieved on 2026-10-03 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 (saframycin A) ↗ MediaIngredientMech (naturalproductmech:mibig-5a2b2bf988) ↗ TaxonMech: Streptomyces lavendulae (NCBITaxon:1914) ↗ PathwayMech (mibig:BGC0000422) ↗

Provenance

Source concept	Source	Version
BGC0000422	MIBIG	5

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