CDA1b

naturalproductmech:mibig-c9928f3f0b 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	LUYIOBWFMDELAR-NMJWYASFSA-N
SMILES	O=C(N[C@@H](CC(O)=O)C(N[C@H](C1=CC=C(O)C=C1)C(N[C@@H](CC(O)=O)C(NCC(N[C@@H](C(N[C@@H](CCC(O)=O)C(N[C@@H](CC2=CNC3=C2C=CC=C3)C(O[C@H](C)[C@@H]4NC([C@H](CO)NC(C(O5)C5CCC)=O)=O)=O)=O)=O)[C@H](OP(O)(O)=O)C(N)=O)=O)=O)=O)=O)[C@H](CC(O)=O)NC([C@@H](CC6=CNC7=C6C=CC=C7)NC4=O)=O
Stereochemistry	undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers

Filing pathway

Unclassified — 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 coelicolor A3(2) NCBITaxon:100226	BGC_CHARACTERIZED	mibig:BGC0000315	PMID:12445768

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 albidoflavus NCBITaxon:1886	LOTUS	DOI:10.1002/ANIE.199704981
Streptomyces albidoflavus NCBITaxon:1886	LOTUS	DOI:10.1016/S1074-5521(02)00252-1
Streptomyces coelicolor NCBITaxon:1902	LOTUS	DOI:10.1002/ANIE.199704981
Streptomyces coelicolor NCBITaxon:1902	LOTUS	DOI:10.1016/S1074-5521(02)00252-1

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000315	Streptomyces coelicolor A3(2) NCBITaxon:100226	CLUSTER_DEMONSTRATED	genbank:AL645882.2

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	HmaS 4-hydroxymandelate synthase UniProtKB:Q9Z4X7		CHEBI:15999 → CHEBI:17210	DOI:10.1016/S1074-5521(02)00252-1

Step 1: SCO3229/HmaS is curated as the 4-hydroxymandelate synthase that supplies the L-4-hydroxyphenylglycine branch of CDA1b biosynthesis. HmaS sits at the first step of the pathway from 4-hydroxyphenylpyruvate to 4-hydroxyphenylglycine; the exact SCO3229 4-hydroxyphenylpyruvate to (S)-4-hydroxymandelate reaction is inferred from the HmaS assignment and therefore kept proposed.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 4 nodes, 3 edges

Partial Streptomyces coelicolor CDA1b biosynthesis graph for HmaS-dependent 4-hydroxyphenylglycine precursor supply.

Subject	Predicate	Object	Notes	Evidence
4-hydroxyphenylpyruvic acid	is proposed to be oxidatively decarboxylated by	HmaS	The direct 4-hydroxyphenylpyruvate to (S)-4-hydroxymandelate assignment is inferred for SCO3229/HmaS.	DOI:10.1016/S1074-5521(02)00252-1 https://mibig.secondarymetabolites.org/repository/BGC0000315.5/index.html https://www.uniprot.org/uniprotkb/Q9Z4X7 https://www.ncbi.nlm.nih.gov/protein/CAB38519.1 reference DOI:10.1016/S1074-5521(02)00252-1 evidence type PRIMARY_EXPERIMENT snippet Deletion of SCO3229 (hmaS) notes Hojati et al. identified the Streptomyces coelicolor CDA cluster, deleted hmaS/SCO3229, and restored CDA production in the mutant by feeding 4-hydroxymandelate, 4-hydroxyphenylglyoxylate, or 4-hydroxyphenylglycine. reference https://mibig.secondarymetabolites.org/repository/BGC0000315.5/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-29 notes MIBiG BGC0000315.5 lists CDA1b as a product of the AL645882.2 Streptomyces coelicolor A3(2) cluster characterized by knockout studies. reference https://www.uniprot.org/uniprotkb/Q9Z4X7 evidence type DATABASE_ASSERTION retrieved on 2026-09-29 notes Unreviewed UniProtKB:Q9Z4X7 is Streptomyces coelicolor SCO3229, a 371 aa 4-hydroxyphenylpyruvic acid dioxygenase entry cross-referenced to EMBL AL645882 protein CAB38519.1. reference https://www.ncbi.nlm.nih.gov/protein/CAB38519.1 evidence type DATABASE_ASSERTION snippet putative 4-hydroxyphenylpyruvic acid dioxygenase retrieved on 2026-09-29 notes NCBI GenPept CAB38519.1 is the SCO3229 coding sequence from Streptomyces coelicolor A3(2) and cross-references UniProtKB/TrEMBL Q9Z4X7.
HmaS	is proposed to form	(S)-4-hydroxymandelate	HmaS is curated as the entry enzyme for the CDA 4-hydroxyphenylglycine precursor pathway.	DOI:10.1016/S1074-5521(02)00252-1 https://mibig.secondarymetabolites.org/repository/BGC0000315.5/index.html https://www.uniprot.org/uniprotkb/Q9Z4X7 https://www.ncbi.nlm.nih.gov/protein/CAB38519.1 reference DOI:10.1016/S1074-5521(02)00252-1 evidence type PRIMARY_EXPERIMENT snippet Deletion of SCO3229 (hmaS) notes Hojati et al. identified the Streptomyces coelicolor CDA cluster, deleted hmaS/SCO3229, and restored CDA production in the mutant by feeding 4-hydroxymandelate, 4-hydroxyphenylglyoxylate, or 4-hydroxyphenylglycine. reference https://mibig.secondarymetabolites.org/repository/BGC0000315.5/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-29 notes MIBiG BGC0000315.5 lists CDA1b as a product of the AL645882.2 Streptomyces coelicolor A3(2) cluster characterized by knockout studies. reference https://www.uniprot.org/uniprotkb/Q9Z4X7 evidence type DATABASE_ASSERTION retrieved on 2026-09-29 notes Unreviewed UniProtKB:Q9Z4X7 is Streptomyces coelicolor SCO3229, a 371 aa 4-hydroxyphenylpyruvic acid dioxygenase entry cross-referenced to EMBL AL645882 protein CAB38519.1. reference https://www.ncbi.nlm.nih.gov/protein/CAB38519.1 evidence type DATABASE_ASSERTION snippet putative 4-hydroxyphenylpyruvic acid dioxygenase retrieved on 2026-09-29 notes NCBI GenPept CAB38519.1 is the SCO3229 coding sequence from Streptomyces coelicolor A3(2) and cross-references UniProtKB/TrEMBL Q9Z4X7.
HmaS	is genetically required for biosynthesis of	CDA1b	Deletion of hmaS abolished CDA production, and exogenous 4-hydroxymandelate or downstream pathway intermediates restored it.	DOI:10.1016/S1074-5521(02)00252-1 https://mibig.secondarymetabolites.org/repository/BGC0000315.5/index.html https://www.uniprot.org/uniprotkb/Q9Z4X7 https://www.ncbi.nlm.nih.gov/protein/CAB38519.1 reference DOI:10.1016/S1074-5521(02)00252-1 evidence type PRIMARY_EXPERIMENT snippet Deletion of SCO3229 (hmaS) notes Hojati et al. identified the Streptomyces coelicolor CDA cluster, deleted hmaS/SCO3229, and restored CDA production in the mutant by feeding 4-hydroxymandelate, 4-hydroxyphenylglyoxylate, or 4-hydroxyphenylglycine. reference https://mibig.secondarymetabolites.org/repository/BGC0000315.5/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-29 notes MIBiG BGC0000315.5 lists CDA1b as a product of the AL645882.2 Streptomyces coelicolor A3(2) cluster characterized by knockout studies. reference https://www.uniprot.org/uniprotkb/Q9Z4X7 evidence type DATABASE_ASSERTION retrieved on 2026-09-29 notes Unreviewed UniProtKB:Q9Z4X7 is Streptomyces coelicolor SCO3229, a 371 aa 4-hydroxyphenylpyruvic acid dioxygenase entry cross-referenced to EMBL AL645882 protein CAB38519.1. reference https://www.ncbi.nlm.nih.gov/protein/CAB38519.1 evidence type DATABASE_ASSERTION snippet putative 4-hydroxyphenylpyruvic acid dioxygenase retrieved on 2026-09-29 notes NCBI GenPept CAB38519.1 is the SCO3229 coding sequence from Streptomyces coelicolor A3(2) and cross-references UniProtKB/TrEMBL Q9Z4X7.

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

Explore across X-Mech

AntibioticMech (CDA1b) ↗ MediaIngredientMech (naturalproductmech:mibig-c9928f3f0b) ↗ TaxonMech: Streptomyces coelicolor A3(2) (NCBITaxon:100226) ↗ PathwayMech (mibig:BGC0000315) ↗

Provenance

Source concept	Source	Version
BGC0000315	MIBIG	5

This page is generated from data/natural_products/unclassified/cda1b.yaml, which is generated from the committed inventories. Neither is edited by hand.