linearmycin B

naturalproductmech:mibig-b37b4ebb26 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	DHFLEVLIHWJIAE-OTPULODUSA-N
SMILES	CC(/C=C/CC/C=C/C=C/C=C/C=C/C=C(\C)/C(=O)O)C(C(C)C(/C=C/C=C/C=C/C=C/C=C/CC(C(C)C(=O)CC(CC(CC(/C=C/CC(CC(CC(CC(/C=C/CC(/C=C/CC(CC(CCCN)O)O)O)O)O)O)O)O)O)O)O)O)O
Stereochemistry	undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers
Cross-references	pubchem:10328913, npatlas:NPA005208

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, 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 sp. Mg1 NCBITaxon:465541	BGC_CHARACTERIZED	mibig:BGC0002072	PMID:28919037

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
Streptomyces NCBITaxon:1883	LOTUS	DOI:10.1039/P19960002315

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0002072	Streptomyces sp. Mg1 NCBITaxon:465541	CLUSTER_DEMONSTRATED	genbank:CP011664.1

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	LnyI ACP S-malonyltransferase NCBIProtein:AKL64828.1		ungrounded → ungrounded	DOI:10.1016/j.chembiol.2017.08.008

Step 1: This curates Streptomyces sp. Mg1 lnyI/AKL64828.1 as a required acyltransferase for the proposed aminoalkyl starter-unit branch of BGC0002072 linearmycin B biosynthesis. The exact AKL64828.1 GenPept accession did not resolve in UniProtKB exact accession, locus-tag, or lnyI searches on 2026-09-27, so enzyme_id is grounded to the native GenPept accession NCBIProtein:AKL64828.1 (UniParc UPI00017E925A maps only to retired/obsolete UniProtKB/TrEMBL entry B4VDY5.1).

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 3 nodes, 2 edges

Partial Streptomyces sp. Mg1 linearmycin B biosynthesis graph for the LnyI acyltransferase requirement in the proposed aminoalkyl starter-unit branch.

Subject	Predicate	Object	Notes	Evidence
LnyI ACP S-malonyltransferase	is required for	aminoalkyl starter-unit biosynthesis	The primary paper showed that lnyI deletion abolished linearmycin production and that lnyI complementation restored production; it further placed LnyI among predicted arginine-derived aminoalkyl starter-unit biosynthesis enzymes. This edge does not assert an assayed acyl-transfer substrate.	DOI:10.1016/j.chembiol.2017.08.008 mibig:BGC0002072 https://www.ncbi.nlm.nih.gov/protein/AKL64828.1 https://www.uniprot.org/uniparc/UPI00017E925A https://www.ncbi.nlm.nih.gov/nuccore/CP011664.1 reference DOI:10.1016/j.chembiol.2017.08.008 evidence type PRIMARY_EXPERIMENT snippet no linearmycins were produced notes Hoefler et al. replaced the Streptomyces sp. Mg1 lnyI acyltransferase open reading frame with an apramycin resistance marker, observed by HPLC that the mutant no longer produced linearmycin A/B/C, and restored linearmycin production by native-promoter lnyI complementation. reference mibig:BGC0002072 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 notes MIBiG BGC0002072 version 3 names linearmycin B as an exact product of the Streptomyces sp. Mg1 type I PKS cluster on CP011664.1 and records knock-out support for the locus. reference https://www.ncbi.nlm.nih.gov/protein/AKL64828.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet ACP S-malonyltransferase notes NCBI GenPept AKL64828.1 is the 345 aa lnyI/M444_04805 protein from Streptomyces sp. Mg1 and is encoded by CP011664.1:1076160..1077197. Exact AKL64828.1, M444_04805, and lnyI UniProtKB searches did not resolve an exact Mg1 accession on 2026-09-27. reference https://www.uniprot.org/uniparc/UPI00017E925A evidence type DATABASE_ASSERTION retrieved on 2026-10-23 snippet AKL64828.1 notes UniParc UPI00017E925A archives the exact 345 aa Streptomyces sp. Mg1 lnyI/M444_04805 sequence (EMBL CP011664.1:1076160..1077197, protein AKL64828.1) and records that UniProtKB/TrEMBL entry B4VDY5.1 is inactive/obsolete, confirming no active UniProtKB accession resolves for AKL64828.1. reference https://www.ncbi.nlm.nih.gov/nuccore/CP011664.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet Streptomyces sp. Mg1 notes GenBank CP011664.1 is the complete Streptomyces sp. Mg1 genome used by BGC0002072; within that genome, lnyI/M444_04805 occupies 1076160..1077197 and encodes AKL64828.1.
aminoalkyl starter-unit biosynthesis	contributes to	linearmycin B	The paper proposed that an aminoalkyl starter unit originating from arginine feeds the linearmycin assembly line to produce linearmycin B. Downstream polyketide chain extension and tailoring steps remain unexpanded.	DOI:10.1016/j.chembiol.2017.08.008 mibig:BGC0002072 https://www.ncbi.nlm.nih.gov/protein/AKL64828.1 https://www.uniprot.org/uniparc/UPI00017E925A https://www.ncbi.nlm.nih.gov/nuccore/CP011664.1 reference DOI:10.1016/j.chembiol.2017.08.008 evidence type PRIMARY_EXPERIMENT snippet no linearmycins were produced notes Hoefler et al. replaced the Streptomyces sp. Mg1 lnyI acyltransferase open reading frame with an apramycin resistance marker, observed by HPLC that the mutant no longer produced linearmycin A/B/C, and restored linearmycin production by native-promoter lnyI complementation. reference mibig:BGC0002072 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 notes MIBiG BGC0002072 version 3 names linearmycin B as an exact product of the Streptomyces sp. Mg1 type I PKS cluster on CP011664.1 and records knock-out support for the locus. reference https://www.ncbi.nlm.nih.gov/protein/AKL64828.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet ACP S-malonyltransferase notes NCBI GenPept AKL64828.1 is the 345 aa lnyI/M444_04805 protein from Streptomyces sp. Mg1 and is encoded by CP011664.1:1076160..1077197. Exact AKL64828.1, M444_04805, and lnyI UniProtKB searches did not resolve an exact Mg1 accession on 2026-09-27. reference https://www.uniprot.org/uniparc/UPI00017E925A evidence type DATABASE_ASSERTION retrieved on 2026-10-23 snippet AKL64828.1 notes UniParc UPI00017E925A archives the exact 345 aa Streptomyces sp. Mg1 lnyI/M444_04805 sequence (EMBL CP011664.1:1076160..1077197, protein AKL64828.1) and records that UniProtKB/TrEMBL entry B4VDY5.1 is inactive/obsolete, confirming no active UniProtKB accession resolves for AKL64828.1. reference https://www.ncbi.nlm.nih.gov/nuccore/CP011664.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet Streptomyces sp. Mg1 notes GenBank CP011664.1 is the complete Streptomyces sp. Mg1 genome used by BGC0002072; within that genome, lnyI/M444_04805 occupies 1076160..1077197 and encodes AKL64828.1.

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

Elsewhere in the fleet

PathwayMech — MIBiG:BGC0002072 (biosynthesized by, same mibig product: mibig:bgc0002072, product linearmycin b; same source taxon ncbitaxon:465541. this links the product to its cluster, not to every producer.)

Explore across X-Mech

AntibioticMech (linearmycin B) ↗ MediaIngredientMech (naturalproductmech:mibig-b37b4ebb26) ↗ TaxonMech: Streptomyces sp. Mg1 (NCBITaxon:465541) ↗ PathwayMech (mibig:BGC0002072) ↗

Provenance

Source concept	Source	Version
BGC0002072	MIBIG	3

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