NaturalProductMech

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cittilin B

naturalproductmech:mibig-5cf4c39e1c 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 InChIKeyLRYMXYNLAMRRTH-CIWZQKDMSA-N
SMILESCC[C@H](C)[C@@H]1NC(=O)[C@@H](N)CC2=CC(=C(O)C=C2)C2=C(O)C3=CC(=C2)C[C@H](NC1=O)C(=O)N[C@H](C(=O)O)CC1=CC=C(C=C1)O3
Stereochemistryfully defined
Cross-referencesnpatlas:NPA032063

Filing pathway

Amino acids and peptides — 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 ribosomal, 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.

TaxonBasisClusterEvidence
Myxococcus xanthus DK 1622
NCBITaxon:246197		 BGC_CHARACTERIZED mibig:BGC0002043 PMID:32639716

Occurrences 2

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.

TaxonSourceReference
Streptomyces
NCBITaxon:1883		 LOTUS DOI:10.7164/ANTIBIOTICS.51.512
Myxococcus xanthus
NCBITaxon:34		 LOTUS DOI:10.1021/ACSCHEMBIO.0C00430

Biosynthetic gene clusters 1

AccessionHostLocus evidenceGenome
mibig:BGC0002043 Myxococcus xanthus DK 1622
NCBITaxon:246197 		CLUSTER_DEMONSTRATED genbank:MN731368.1

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.

StepEnzymeReactionSubstrate → productEvidence
1 CitB native DK1622 reference
NCBIProtein:QLH55579.1		 ungrounded → naturalproductmech:mibig-5cf4c39e1c https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000426.json
2 CitC native DK1622 reference
UniProtKB:Q1DEH3		 naturalproductmech:mibig-5cf4c39e1c → naturalproductmech:mibig-9e3bd2912f https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000425.json

Step 1: MITE0000426-reported CitB cytochrome P450 precursor crosslinking and MxPep leader removal maturing the CitA precursor peptide (NCBIProtein:QLH55578.1) to cittilin B on MN731368.1 (BGC0002043). Synchronizes biosynthetic_pathway with the existing MITE-backed causal_graph without upgrading producer or locus evidence grades.

Step 2: MITE0000425-reported O-methylation of cittilin B to cittilin A by CitC (UniProtKB:Q1DEH3, QLH55580.1 on MN731368.1, BGC0002043; DK1622 locus MXAN_0682 / ABF85961.1 on CP000113.1). Synchronizes biosynthetic_pathway with the existing MITE-backed causal_graph without upgrading producer or locus evidence grades.

Mechanism & Biosynthesis Overview

PRODUCERS & OCCURRENCE 1 producer (1 causal) 2 cited occurrences BIOSYNTHETIC LOCUS 1 gene cluster 2 curated pathway steps NATURAL PRODUCT cittilin B naturalproductmech:mibig-5cf4c39e1c Amino acids and peptides TARGETS & BIOACTIVITY 0 molecular targets 0 bioactivities · 2 graphs

Causal graph — biosynthesis 7 nodes, 6 edges

MITE-narrated CitB precursor crosslinking followed by MxPep-mediated leader removal to yield the intermediate cittilin B. Separate database assertions, not a CitB-alone free-product assay. CitB and the unmodified precursor have sequence-verified native DK1622 references; the CitA alias is a curator mapping, not an assay-stock claim. MxPep and the modified precursor remain ungrounded. No primary assay, physical complex or pathway finality is inferred; not full-record sign-off.

SubjectPredicateObjectNotesEvidence
CitB native DK1622 reference is_database_reported_catalyst_of MITE-reported CitB precursor crosslinking The assigned reaction is oxidative C-C and C-O crosslink formation in the precursor core. No native heme/iron occupancy, electron donor, binding site, kinetics, knockout phenotype or physical complex is inferred.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000426.json
https://www.ncbi.nlm.nih.gov/protein/QLH55579.1
https://www.ncbi.nlm.nih.gov/nuccore/MN731368.1
https://www.uniprot.org/uniparc/UPI0002F6195D
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000426.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    MITE0000426 version 1, active, names CitB/QLH55579.1, UniParc UPI0002F6195D and BGC0002043. Its narrative assigns precursor crosslinking to CitB and leader removal to MxPep. Assay and knockout codes remain database assertions; the cited primary paper was inaccessible. No independently inspected primary assay.
    snippet
    within the CitA precursor peptide
  • reference
    https://www.ncbi.nlm.nih.gov/protein/QLH55579.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Complete independent GenPept cytochrome P450 reference, 450 residues, Myxococcus xanthus DK1622/taxon246197; full coded_by inspected. Reference identity does not identify a historical assay stock or construct.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/MN731368.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-07
    notes
    Full1353-nt plus-strand CDS11483..12835, codon1/table11, translates exactly to annotation, independent QLH55579.1 and UniParc, all450aa. Independent coded_by DNA/coordinates and DK1622/taxon246197 source match. This verifies reference sequence identity, not catalytic activity.
  • reference
    https://www.uniprot.org/uniparc/UPI0002F6195D
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Retained450-residue archive has no active UniProtKB cross-reference. A0A7D5SGQ7 and A0AA46PCU6 are inactive, not selected as current UniProt examples. UniParc is not UniProtKB; this bounded archive result does not establish universal UniProt absence.
CitA unmodified precursor, native DK1622 reference is_database_reported_substrate_of MITE-reported CitB precursor crosslinking The native unmodified27-aa reference MKKALYSLAVLMRFARADKLSAPYIYY contains the database-narrated YIYY core; it is not the free tetrapeptide or the modified precursor state. CitA alias assignment is curator-inferred, while function remains MITE's database assertion. No historical assay stock, construct or exact leader-cleavage site is established. The encoded free tetrapeptide example does not prove that leader-free substrate was assayed with CitB alone.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000426.json
https://www.ncbi.nlm.nih.gov/protein/QLH55578.1
https://www.ncbi.nlm.nih.gov/nuccore/MN731368.1
https://www.uniprot.org/uniparc/UPI001751B65D
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000426.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    MITE0000426 version 1, active, names CitB/QLH55579.1, UniParc UPI0002F6195D and BGC0002043. Its narrative assigns precursor crosslinking to CitB and leader removal to MxPep. Assay and knockout codes remain database assertions; the cited primary paper was inaccessible. No independently inspected primary assay.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/QLH55578.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    snippet
    cittilin precursor peptide
    notes
    Complete27-aa native DK1622/taxon246197 reference. No native gene qualifier. Full coded_by inspected; sequence reference only, not an assay-stock or construct identity.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/MN731368.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-07
    notes
    Full84-nt plus-CDS11281..11364, codon1/table11, matches annotation, independent QLH55578.1 and UniParc, all27aa. Exact coded_by DNA/coordinates and DK1622/taxon246197 agree. CitA alias mapping uses the native cittilin-precursor annotation, same BGC0002043 and terminal YIYY core with MITE's narrative; not a native gene-name assertion or historical assay proof. MN731368.1 is a21261-bp BGC sequence, not a full genome.
  • reference
    https://www.uniprot.org/uniparc/UPI001751B65D
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Exact27-aa archive with active EMBL QLH55578 version1/taxon246197. All three listed UniProtKB references are inactive: A0A7D5NMR6, A0A7D5NMW3 and native-strain A0A7D5SLS4. None selected as current UniProt. Official accession QLH55578 and gene_exact:citA/organism_id:246197 searches returned zero results; bounded queries/archive only, not universal absence. UniParc is not UniProtKB.
MITE-reported CitB precursor crosslinking has_database_narrated_precursor_product Crosslinked CitA precursor, database narrative An ungrounded precursor state represents the database narrative before leader removal, not an independently isolated or chemically resolved intermediate. It is not identified with free cittilin B.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000426.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000426.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    MITE0000426 version 1, active, names CitB/QLH55579.1, UniParc UPI0002F6195D and BGC0002043. Its narrative assigns precursor crosslinking to CitB and leader removal to MxPep. Assay and knockout codes remain database assertions; the cited primary paper was inaccessible. No independently inspected primary assay.
MxPep, database-named maturation protein is_database_reported_catalyst_of MITE-reported MxPep leader removal MITE names MxPep for maturation but provides no MxPep accession in this entry. No arbitrary protease homolog, native strain mapping, exact cleavage site, construct, assay or physical association with CitB is adopted.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000426.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000426.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    MITE0000426 version 1, active, names CitB/QLH55579.1, UniParc UPI0002F6195D and BGC0002043. Its narrative assigns precursor crosslinking to CitB and leader removal to MxPep. Assay and knockout codes remain database assertions; the cited primary paper was inaccessible. No independently inspected primary assay.
    snippet
    by removing the leader sequence
Crosslinked CitA precursor, database narrative is_database_narrated_substrate_of MITE-reported MxPep leader removal This order follows the source narrative, not genomic gene order or an independently inspected time-course. No additional processing step is inferred.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000426.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000426.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    MITE0000426 version 1, active, names CitB/QLH55579.1, UniParc UPI0002F6195D and BGC0002043. Its narrative assigns precursor crosslinking to CitB and leader removal to MxPep. Assay and knockout codes remain database assertions; the cited primary paper was inaccessible. No independently inspected primary assay.
MITE-reported MxPep leader removal has_database_reported_product cittilin B MITE names cittilin B as an intermediate and encodes a product matching owner full key LRYMXYNLAMRRTH-CIWZQKDMSA-N and complete stereo in the pinned repository-helper/RDKit2026.03.5 screen. This supports product correspondence, not a CitB-only assay. Cittilin A, its separate CitC graph, all source fields, BGC_CHARACTERIZED/CLUSTER_DEMONSTRATED grades and occurrences are unchanged. No pathway finality or producer upgrade is inferred.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000426.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000426.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    MITE0000426 version 1, active, names CitB/QLH55579.1, UniParc UPI0002F6195D and BGC0002043. Its narrative assigns precursor crosslinking to CitB and leader removal to MxPep. Assay and knockout codes remain database assertions; the cited primary paper was inaccessible. No independently inspected primary assay.

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

Causal graph — biosynthesis 4 nodes, 3 edges

Substrate-owner context for MITE-reported CitC O-methylation of cittilin B to cittilin A. CitC is already represented on the product owner; this is not a new global protein or assay. Exact neutral compound forms match the database example. Native-reference identity does not establish experimental function. Existing CitB/MxPep maturation and CitA grounding are preserved separately; no physical assembly or cross-graph edge is inferred.

SubjectPredicateObjectNotesEvidence
CitC native DK1622 reference is_database_reported_catalyst_of MITE-reported CitC O-methylation MITE supplies the functional attribution; reference translation establishes identity only. No primary assay, rate, knockout phenotype, native cofactor state, site or physical complex is adopted. Automated ubiquinone/mitochondrial family labels are not cittilin chemistry.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000425.json
https://www.uniprot.org/uniprotkb/Q1DEH3
https://www.uniprot.org/uniparc/UPI00004FDDBF
https://www.ncbi.nlm.nih.gov/protein/QLH55580.1
https://www.ncbi.nlm.nih.gov/nuccore/MN731368.1
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000425.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    MITE0000425 version 1, active, identifies CitC, QLH55580.1/UniParc UPI00004FDDBF and BGC0002043, and assigns O-methylation of cittilin B to yield cittilin A. Its heterologous-expression and in-vitro codes are database assertions: the cited primary paper was inaccessible. No specific assay, kinetic or native cofactor claim is adopted.
    snippet
    CitC specifically methylates cittilin B
  • reference
    https://www.uniprot.org/uniprotkb/Q1DEH3
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Current TrEMBL entry103, sequence1,204aa, MXAN_0682/taxon246197, predicted protein existence, no FUNCTION or catalytic-activity comment. The generic methyltransferase-domain name and automated keywords are not independent cittilin evidence. Entry cross-links CP000113/ABF85961.1, not directly MN731368/QLH55580.1; exact full sequence, strain and UniParc provide the mapping.
  • reference
    https://www.uniprot.org/uniparc/UPI00004FDDBF
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Retained full sequence archive links active Q1DEH3 and QLH55580 to the same204-residue DK1622 reference. Inactive UniProt entries and other-strain identical sequences are not selected as tested examples. UniParc is not a UniProtKB accession.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/QLH55580.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Complete independent GenPept methyltransferase record and coded_by inspected:204aa, M.xanthus DK1622/taxon246197; no named CitC gene qualifier is required to replace the exact protein mapping.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/MN731368.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-07
    notes
    Complete615-nt plus-strand CDS12819..13433, codon1/table11, translates exactly to annotation, independent QLH55580.1, UniParc and current Q1DEH3, all204aa. Independent coded_by DNA/coordinates and genomic/source strain DK1622/taxon246197 match. No separate ABF85961.1/CP000113 native-CDS check or historical assay-stock/construct identity is claimed.
cittilin B is_database_reported_substrate_of MITE-reported CitC O-methylation Pinned MITE substrate matches this cittilin B owner's full InChIKey LRYMXYNLAMRRTH-CIWZQKDMSA-N and complete stereo in the verified repository-helper/RDKit2026.03.5 calculation. This is the exact neutral substrate, not the CitA precursor or a different congener. The existing CitB/MxPep maturation graph and its CitA grounding are unchanged.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000425.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000425.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    MITE0000425 version 1, active, identifies CitC, QLH55580.1/UniParc UPI00004FDDBF and BGC0002043, and assigns O-methylation of cittilin B to yield cittilin A. Its heterologous-expression and in-vitro codes are database assertions: the cited primary paper was inaccessible. No specific assay, kinetic or native cofactor claim is adopted.
MITE-reported CitC O-methylation has_database_reported_product cittilin A Pinned MITE product matches the separate cittilin A owner's full InChIKey WKYLONYSKYXJSJ-UJGPGMDKSA-N and complete stereo in the verified repository-helper/RDKit2026.03.5 calculation. That owner and its CitC graph remain unchanged. No pathway finality, primary assay or producer upgrade; existing source grades are preserved.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000425.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000425.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    MITE0000425 version 1, active, identifies CitC, QLH55580.1/UniParc UPI00004FDDBF and BGC0002043, and assigns O-methylation of cittilin B to yield cittilin A. Its heterologous-expression and in-vitro codes are database assertions: the cited primary paper was inaccessible. No specific assay, kinetic or native cofactor claim is adopted.

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

Explore across X-Mech

AntibioticMech (cittilin B) ↗ MediaIngredientMech (naturalproductmech:mibig-5cf4c39e1c) ↗ TaxonMech: Myxococcus xanthus DK 1622 (NCBITaxon:246197) ↗ PathwayMech (mibig:BGC0002043) ↗

Provenance

Source conceptSourceVersion
BGC0002043MIBIG3

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