erythromycin D

CHEBI:28331 EXACT SEEDED antimicrobial unspecified

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	CLQUUOKNEOQBSW-KEGKUKQHSA-N
SMILES	CC[C@@H]1[C@@H]([C@@H]([C@H](C(=O)[C@@H](C[C@@]([C@@H]([C@H]([C@@H]([C@H](C(=O)O1)C)O[C@H]2C[C@@]([C@H]([C@@H](O2)C)O)(C)O)C)O[C@H]3[C@@H]([C@H](C[C@H](O3)C)N(C)C)O)(C)O)C)C)O)C
Stereochemistry	fully defined
Cross-references	pubchem:24755489

Filing pathway

Polyketides — 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 pks, saccharide, 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
Saccharopolyspora erythraea NRRL 2338 NCBITaxon:405948	BGC_CHARACTERIZED	mibig:BGC0000055	PMID:11336289

Occurrences 0

None cited.

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000055	Saccharopolyspora erythraea NRRL 2338 NCBITaxon:405948	CLUSTER_DEMONSTRATED	genbank:AM420293.1

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
10	EryF 6-deoxyerythronolide B hydroxylase UniProtKB:Q00441	RHEA:40299	CHEBI:16089 → CHEBI:27977	DOI:10.1128/jb.174.3.725-735.1992
20	EryK erythromycin C-12 hydroxylase UniProtKB:P48635	RHEA:32631	CHEBI:63677 → CHEBI:64258	DOI:10.1021/bi00006a006
30	EryG erythromycin 3''-O-methyltransferase UniProtKB:A4F7P5	RHEA:32651	CHEBI:63677 → CHEBI:64279	DOI:10.1128/jb.172.5.2541-2546.1990

Step 10: Partial tailoring view: EryF hydroxylates 6-deoxyerythronolide B to erythronolide B; uncurated glycosylation and deoxysugar steps between erythronolide B and erythromycin D are intentionally omitted.

Step 20: EryK hydroxylates erythromycin D to erythromycin C. The erythromycin B branch is excluded here because EryK does not accept erythromycin B efficiently.

Step 30: Saccharopolyspora erythraea NRRL 2338 SACE_0728 EryG O-methylates the 3''-hydroxyl of the mycarose moiety of erythromycin D to form erythromycin B. RHEA:32651 uses protonated CHEBI:63677 erythromycin D(1+) and CHEBI:64279 erythromycin B(1+) as reaction participants corresponding to neutral records CHEBI:28331 and CHEBI:28196.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 8 nodes, 6 edges

Partial Saccharopolyspora erythraea NRRL 2338 BGC0000055 macrolide tailoring graph around erythromycin D (intermediate glycosylation steps between erythronolide B and erythromycin D intentionally omitted): upstream EryF 6-deoxyerythronolide B C-6 hydroxylation and branching downstream conversion of erythromycin D by EryK (to erythromycin C) and EryG (to erythromycin B).

Subject	Predicate	Object	Notes	Evidence
6-deoxyerythronolide B	is hydroxylated by	EryF 6-deoxyerythronolide B hydroxylase		DOI:10.1128/jb.174.3.725-735.1992 reference DOI:10.1128/jb.174.3.725-735.1992 evidence type PRIMARY_EXPERIMENT notes EryF catalyzes RHEA:40299.
EryF 6-deoxyerythronolide B hydroxylase	forms	erythronolide B	The full DEBS-to-glycosylated-macrolide route between erythronolide B and erythromycin D remains uncurated in this partial graph.	DOI:10.1128/jb.174.3.725-735.1992 reference DOI:10.1128/jb.174.3.725-735.1992 evidence type PRIMARY_EXPERIMENT notes EryF catalyzes RHEA:40299.
erythromycin D	is hydroxylated by	EryK erythromycin C-12 hydroxylase		DOI:10.1021/bi00006a006 reference DOI:10.1021/bi00006a006 evidence type PRIMARY_EXPERIMENT notes EryK catalyzes RHEA:32631.
EryK erythromycin C-12 hydroxylase	forms	erythromycin C		DOI:10.1021/bi00006a006 reference DOI:10.1021/bi00006a006 evidence type PRIMARY_EXPERIMENT notes EryK catalyzes RHEA:32631.
erythromycin D	is O-methylated by	EryG erythromycin 3''-O-methyltransferase	RHEA:32651 consumes S-adenosyl-L-methionine and erythromycin D(1+) along the EryG branch to erythromycin B.	DOI:10.1128/jb.172.5.2541-2546.1990 DOI:10.1021/bi00006a006 https://mibig.secondarymetabolites.org/repository/BGC0000055.5/BGC0000055.gbk https://www.uniprot.org/uniprotkb/A4F7P5 https://www.rhea-db.org/rhea/32651 reference DOI:10.1128/jb.172.5.2541-2546.1990 evidence type PRIMARY_EXPERIMENT snippet eryG codes for the structural gene of this enzyme notes Paulus et al. sequenced the Saccharopolyspora erythraea eryG region and showed in Escherichia coli that eryG encodes S-adenosylmethionine:erythromycin C/D O-methyltransferase converting erythromycin D to erythromycin B and erythromycin C to erythromycin A. reference DOI:10.1021/bi00006a006 evidence type PRIMARY_EXPERIMENT snippet preference of the enzyme for ErD over the alternative C-12 hydroxylase substrate ErB notes Lambalot et al. characterized the branched late erythromycin pathway in Saccharopolyspora erythraea where erythromycin D is either C-12 hydroxylated by EryK to erythromycin C or 3''-O-methylated by EryG to erythromycin B. reference https://mibig.secondarymetabolites.org/repository/BGC0000055.5/BGC0000055.gbk evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes MIBiG BGC0000055.5 lists the Saccharopolyspora erythraea NRRL 2338 SACE_0730 eryF, SACE_0728 eryG, and SACE_0713 eryK tailoring genes for erythromycins A, B, C, and D. reference https://www.uniprot.org/uniprotkb/A4F7P5 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes Reviewed UniProtKB:A4F7P5 is the Saccharopolyspora erythraea NRRL 2338 SACE_0728 eryG O-methyltransferase and annotates EC:2.1.1.254 with RHEA:32647 (erythromycin C to A) and RHEA:32651 (erythromycin D to B). reference https://www.rhea-db.org/rhea/32651 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes RHEA:32651 is the EC:2.1.1.254 reaction S-adenosyl-L-methionine + erythromycin D(1+) = S-adenosyl-L-homocysteine + erythromycin B(1+) + H+.
EryG erythromycin 3''-O-methyltransferase	forms	erythromycin B(1+)	RHEA:32651 produces CHEBI:64279 erythromycin B(1+), the protonated conjugate acid of sibling record CHEBI:28196 erythromycin B.	DOI:10.1128/jb.172.5.2541-2546.1990 DOI:10.1021/bi00006a006 https://mibig.secondarymetabolites.org/repository/BGC0000055.5/BGC0000055.gbk https://www.uniprot.org/uniprotkb/A4F7P5 https://www.rhea-db.org/rhea/32651 reference DOI:10.1128/jb.172.5.2541-2546.1990 evidence type PRIMARY_EXPERIMENT snippet eryG codes for the structural gene of this enzyme notes Paulus et al. sequenced the Saccharopolyspora erythraea eryG region and showed in Escherichia coli that eryG encodes S-adenosylmethionine:erythromycin C/D O-methyltransferase converting erythromycin D to erythromycin B and erythromycin C to erythromycin A. reference DOI:10.1021/bi00006a006 evidence type PRIMARY_EXPERIMENT snippet preference of the enzyme for ErD over the alternative C-12 hydroxylase substrate ErB notes Lambalot et al. characterized the branched late erythromycin pathway in Saccharopolyspora erythraea where erythromycin D is either C-12 hydroxylated by EryK to erythromycin C or 3''-O-methylated by EryG to erythromycin B. reference https://mibig.secondarymetabolites.org/repository/BGC0000055.5/BGC0000055.gbk evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes MIBiG BGC0000055.5 lists the Saccharopolyspora erythraea NRRL 2338 SACE_0730 eryF, SACE_0728 eryG, and SACE_0713 eryK tailoring genes for erythromycins A, B, C, and D. reference https://www.uniprot.org/uniprotkb/A4F7P5 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes Reviewed UniProtKB:A4F7P5 is the Saccharopolyspora erythraea NRRL 2338 SACE_0728 eryG O-methyltransferase and annotates EC:2.1.1.254 with RHEA:32647 (erythromycin C to A) and RHEA:32651 (erythromycin D to B). reference https://www.rhea-db.org/rhea/32651 evidence type DATABASE_ASSERTION retrieved on 2026-10-01 notes RHEA:32651 is the EC:2.1.1.254 reaction S-adenosyl-L-methionine + erythromycin D(1+) = S-adenosyl-L-homocysteine + erythromycin B(1+) + H+.

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

Elsewhere in the fleet

AntibioticMech — CHEBI:28331 (same structure, same inchikey)

Explore across X-Mech

AntibioticMech (erythromycin D) ↗ MediaIngredientMech (CHEBI:28331) ↗ TaxonMech: Saccharopolyspora erythraea NRRL 2338 (NCBITaxon:405948) ↗ PathwayMech (mibig:BGC0000055) ↗

Provenance

Source concept	Source	Version
BGC0000055	MIBIG	5
CHEBI:28331	CHEBI	3-star

This page is generated from data/natural_products/polyketides/erythromycin-d.yaml, which is generated from the committed inventories. Neither is edited by hand.