lomaiviticin C

naturalproductmech:mibig-5a11cea583 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	ZFPVZBQTCYDNIT-GTOFKKLISA-N
SMILES	O=C([C@@]([C@@]([C@@](O[C@H]1C[C@H](OC)[C@@H](O)[C@H](C)O1)(CC)[C@@H]2O[C@@H]3C[C@H](O)[C@@H](N(C)C)[C@H](C)O3)([H])C(C(C4=C5C(C6=C(O)C=CC(O)=C6C4=O)=O)=C2C5=[N+]=[N-])=O)([H])[C@@](O[C@@H]7O[C@@H](C)[C@H](O)[C@@H](OC)C7)(CC)[C@@H]8O[C@@H]9C[C@H](O)[C@@H](N(C)C)[C@H](C)O9)C%10=C8C=C%11C%10=C(O)C%12=C(O)C=CC(O)=C%12C%11=O
Stereochemistry	fully defined

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
Salinispora pacifica Strain: DPJ-0016 NCBITaxon:351187	SOURCE_ASSERTION	mibig:BGC0000240	DOI:10.1016/j.tet.2014.03.009 reference DOI:10.1016/j.tet.2014.03.009 evidence type DATABASE_ASSERTION notes MIBiG BGC0000240 entry version 5; claim-specific citation selected through a reviewed producer_reference correction. This remains a database assertion, not independently graded experimental evidence. reference DOI:10.1016/j.tet.2014.03.009 evidence type CURATOR_INFERENCE notes Curated exclusion of source locus methods from this taxon/locus claim: Knock-out studies\|Enzymatic assays. KF731828.1 is DPJ-0016. Janso disrupts lom58 in DPJ-0019/KF515737.1; Waldman assays DPJ-0019 Lom62/Lom63; PMID:23649992 studies CNB-440. These experiments do not grade the deposited DPJ-0016 locus. Retain its source assertion and separately qualify reported DPJ-0016 C production without claiming the disputed stored encoding is correct. No locus, taxon or chemistry replacement. See #977; identity remains open in #975. Curator: codex; date: 2026-10-14. reference DOI:10.1016/j.tet.2014.03.009 evidence type CURATOR_INFERENCE notes Citation routing only. PMID:23649992 concerns CNB-440, not DPJ-0016. Janso explicitly reports DPJ-0016 C production and maps its locus to KF731828. Route the producer citation to that study and the deposited locus citation to its sequence record; DPJ-0019 knockout and enzyme experiments are separately excluded from this locus grade. Exact C structure remains unresolved in #975; routing does not certify the stored encoding. See #977. Original imported citation PMID:23649992 (ENTRY) remains in the raw inventory, not as support for this claim. MIBiG source row BGC0000240:2; SHA256 304afb17b8c77fa669e0b4b6b2a9bd2b6168d2977e02256c188d0522137b6529. Curator: codex; date: 2026-10-14. Taxon, locus, chemistry and evidence grades are unchanged. reference DOI:10.1016/j.tet.2014.03.009 evidence type CURATOR_INFERENCE notes Strain context: DPJ-0016. Janso explicitly reports C production in DPJ-0016 (18 mg/L PCAA, 16 mg/L PYE) and maps its locus to KF731828.1. Qualify this C producer only; do not infer DPJ-0016 D production from the deposit. No taxon remapping or evidence upgrade, and the stored exact C structure remains disputed in #975. See #977. Taxon identity and evidence grade are unchanged; this is not a species-wide experiment. MIBiG source row BGC0000240:2; SHA256 304afb17b8c77fa669e0b4b6b2a9bd2b6168d2977e02256c188d0522137b6529. Curator: codex; date: 2026-10-14.

Occurrences 0

None cited.

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000240	Salinispora pacifica NCBITaxon:351187	CLUSTER_UNSTATED	genbank:KF731828.1

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	Lom62 acyltransferase/decarboxylase with Lom63 acyl carrier protein		ungrounded → ungrounded	DOI:10.1021/ol403714g

Step 1: This curates S. pacifica DPJ-0019 Lom62/AHF72798.1 and Lom63/AHF72799.1 as an assayed acyltransferase/decarboxylase plus ACP pair that can generate the proposed propionyl-ACP starter unit for lomaiviticin biosynthesis. The exact DPJ-0019 GenPept accessions did not resolve in UniProtKB exact-accession or KF515737/lom62/lom63 searches on 2026-09-27, so enzyme_id is left unfilled and NCBI Protein records are cited as official sequence evidence. Exact-product identity remains disputed (issue #975). The stored C structure retains a superseded core arrangement; the experimental scaffold/starter evidence does not validate this exact stored encoding.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 4 nodes, 3 edges

Partial S. pacifica lomaiviticin C biosynthesis graph for the proposed Lom62/Lom63 propionyl-ACP starter-unit branch. Exact-product identity is unresolved; see the curator identity discussion.

Subject	Predicate	Object	Notes	Evidence
Lom62 acyltransferase/decarboxylase	catalyzes	propionyl-ACP starter-unit generation	The in vitro assay showed Lom62-dependent propionyl-Lom63 formation from methylmalonyl-CoA; this graph leaves the subsequent propionyl starter-unit transfer to the type II PKS unresolved.	DOI:10.1021/ol403714g https://www.ncbi.nlm.nih.gov/protein/AHF72798.1 https://www.ncbi.nlm.nih.gov/protein/AHF72799.1 https://www.ncbi.nlm.nih.gov/nuccore/KF515737.1 reference DOI:10.1021/ol403714g evidence type PRIMARY_EXPERIMENT snippet Robust, Lom62-dependent formation notes Waldman and Balskus cloned Salinispora pacifica DPJ-0019 lom62, lom60, and lom63, then showed in vitro by HPLC/LC-MS that Lom62 generated the expected propionyl-ACP thioester robustly only with methylmalonyl-CoA and Lom63. reference https://www.ncbi.nlm.nih.gov/protein/AHF72798.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet acyl transferase/decarboxylase notes NCBI GenPept AHF72798.1 is the 324 aa S. pacifica DPJ-0019 lom62 product on KF515737.1:59562..60536; exact AHF72798.1, AHF72798, lom62, and KF515737 UniProtKB searches did not resolve a S. pacifica accession on 2026-09-27. reference https://www.ncbi.nlm.nih.gov/protein/AHF72799.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet phosphopantheine-binding protein notes NCBI GenPept AHF72799.1 is the 107 aa S. pacifica DPJ-0019 lom63 acyl carrier protein on complement(KF515737.1:60555..60878); exact AHF72799.1, AHF72799, lom63, and KF515737 UniProtKB searches did not resolve a S. pacifica accession on 2026-09-27. reference https://www.ncbi.nlm.nih.gov/nuccore/KF515737.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet lomaiviticin biosynthetic gene cluster notes GenBank KF515737.1 is the 72,505 bp S. pacifica DPJ-0019 lomaiviticin biosynthetic gene cluster and carries lom62/AHF72798.1 and lom63/AHF72799.1.
Lom63 acyl carrier protein	is the preferred carrier protein for	propionyl-ACP starter-unit generation	Lom63 is represented as the preferred ACP partner because competition and single-ACP assays favored propionyl-Lom63 formation over Lom60.	DOI:10.1021/ol403714g https://www.ncbi.nlm.nih.gov/protein/AHF72798.1 https://www.ncbi.nlm.nih.gov/protein/AHF72799.1 https://www.ncbi.nlm.nih.gov/nuccore/KF515737.1 reference DOI:10.1021/ol403714g evidence type PRIMARY_EXPERIMENT snippet Robust, Lom62-dependent formation notes Waldman and Balskus cloned Salinispora pacifica DPJ-0019 lom62, lom60, and lom63, then showed in vitro by HPLC/LC-MS that Lom62 generated the expected propionyl-ACP thioester robustly only with methylmalonyl-CoA and Lom63. reference https://www.ncbi.nlm.nih.gov/protein/AHF72798.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet acyl transferase/decarboxylase notes NCBI GenPept AHF72798.1 is the 324 aa S. pacifica DPJ-0019 lom62 product on KF515737.1:59562..60536; exact AHF72798.1, AHF72798, lom62, and KF515737 UniProtKB searches did not resolve a S. pacifica accession on 2026-09-27. reference https://www.ncbi.nlm.nih.gov/protein/AHF72799.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet phosphopantheine-binding protein notes NCBI GenPept AHF72799.1 is the 107 aa S. pacifica DPJ-0019 lom63 acyl carrier protein on complement(KF515737.1:60555..60878); exact AHF72799.1, AHF72799, lom63, and KF515737 UniProtKB searches did not resolve a S. pacifica accession on 2026-09-27. reference https://www.ncbi.nlm.nih.gov/nuccore/KF515737.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet lomaiviticin biosynthetic gene cluster notes GenBank KF515737.1 is the 72,505 bp S. pacifica DPJ-0019 lomaiviticin biosynthetic gene cluster and carries lom62/AHF72798.1 and lom63/AHF72799.1.
propionyl-ACP starter-unit generation	contributes to	lomaiviticin C	Waldman and Balskus proposed Lom62/Lom63 propionyl-ACP formation as lomaiviticin starter-unit logic based on the lomaiviticin scaffold and cluster context; the edge is therefore narrower than a complete pathway from this starter unit to lomaiviticin C. Exact-product identity remains disputed (issue #975). The stored C structure retains a superseded core arrangement; the experimental scaffold/starter evidence does not validate this exact stored encoding.	DOI:10.1021/ol403714g https://www.ncbi.nlm.nih.gov/protein/AHF72798.1 https://www.ncbi.nlm.nih.gov/protein/AHF72799.1 https://www.ncbi.nlm.nih.gov/nuccore/KF515737.1 DOI:10.1021/jacs.1c01729 reference DOI:10.1021/ol403714g evidence type PRIMARY_EXPERIMENT snippet Robust, Lom62-dependent formation notes Waldman and Balskus cloned Salinispora pacifica DPJ-0019 lom62, lom60, and lom63, then showed in vitro by HPLC/LC-MS that Lom62 generated the expected propionyl-ACP thioester robustly only with methylmalonyl-CoA and Lom63. reference https://www.ncbi.nlm.nih.gov/protein/AHF72798.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet acyl transferase/decarboxylase notes NCBI GenPept AHF72798.1 is the 324 aa S. pacifica DPJ-0019 lom62 product on KF515737.1:59562..60536; exact AHF72798.1, AHF72798, lom62, and KF515737 UniProtKB searches did not resolve a S. pacifica accession on 2026-09-27. reference https://www.ncbi.nlm.nih.gov/protein/AHF72799.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet phosphopantheine-binding protein notes NCBI GenPept AHF72799.1 is the 107 aa S. pacifica DPJ-0019 lom63 acyl carrier protein on complement(KF515737.1:60555..60878); exact AHF72799.1, AHF72799, lom63, and KF515737 UniProtKB searches did not resolve a S. pacifica accession on 2026-09-27. reference https://www.ncbi.nlm.nih.gov/nuccore/KF515737.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet lomaiviticin biosynthetic gene cluster notes GenBank KF515737.1 is the 72,505 bp S. pacifica DPJ-0019 lomaiviticin biosynthetic gene cluster and carries lom62/AHF72798.1 and lom63/AHF72799.1. reference DOI:10.1021/jacs.1c01729 evidence type CURATOR_INFERENCE notes The inspected 2021 microED/NMR text revises C core connectivity and secondary glycoside configuration. No replacement key is asserted here.

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

Explore across X-Mech

AntibioticMech (lomaiviticin C) ↗ MediaIngredientMech (naturalproductmech:mibig-5a11cea583) ↗ TaxonMech: Salinispora pacifica (NCBITaxon:351187) ↗ PathwayMech (mibig:BGC0000240) ↗

Open questions 1

curator-lomaiviticin-identity-conflict — Which exact structure is supported for this source product?

Provenance

Source concept	Source	Version
BGC0000240	MIBIG	5

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