NaturalProductMech

Browse · Carbohydrates · desosamine

desosamine

CHEBI:32540 EXACT SEEDED

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 InChIKeyVTJCSBJRQLZNHE-CSMHCCOUSA-N
SMILES[H]C([H])([C@@]([H])(C)O)[C@]([H])(N(C)C)[C@@]([H])(O)C=O
Stereochemistryfully defined

Filing pathway

Carbohydrates — computed by NPClassifier npclassifier.gnps2.org@2026-10-18, which is why it is pinned rather than recomputed. The gene cluster's asserted class is 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.

TaxonBasisClusterEvidence
Streptomyces venezuelae
Strain: ATCC 15439
NCBITaxon:54571		 SOURCE_ASSERTION mibig:BGC0000898
PMID:9770448, DOI:10.1073/pnas.95.21.12111
  • reference
    PMID:9770448
    evidence type
    DATABASE_ASSERTION
    notes
    MIBiG BGC0000898 entry version 5; citation taken from the entry level
  • reference
    PMID:9770448
    evidence type
    CURATOR_INFERENCE
    notes
    Curated structure replacement for MIBiG BGC0000898:1, version 5: HUKYPYXOBINMND-HYUJHOPRSA-N -> CHEBI:32540 (VTJCSBJRQLZNHE-CSMHCCOUSA-N). MIBiG BGC0000898 (AF079762.1; Xue et al., PNAS 1998, PMID:9770448) is the Streptomyces venezuelae des deoxysugar biosynthetic gene cluster and names compound 1 desosamine, but attaches the macrolide glycoside methymycin SMILES (HUKYPYXOBINMND-HYUJHOPRSA-N) and methymycin database xrefs (pubchem:5282034|npatlas:NPA01238), colliding with BGC0000094:1 (methymycin, CHEBI:29630). Split BGC0000898:1 onto the 3-star ChEBI structure for desosamine (CHEBI:32540, VTJCSBJRQLZNHE-CSMHCCOUSA-N) and withhold the methymycin xrefs. Original database_ids withheld: pubchem:5282034|npatlas:NPA01238. Other inventories are joined only on the corrected key, never transferred from the old key. Source row SHA256 1c3876fb6e15ecdbd0e4724f6af87e536ae9e4acdba5b97d7cf5381641555eae; target row SHA256 00c1f34e6e734f1eebb250dc0f09eebbc4e91d08cf291bb678b67e7a38698d62. Curator: claude; date: 2026-10-18.
  • reference
    DOI:10.1073/pnas.95.21.12111
    evidence type
    CURATOR_INFERENCE
    notes
    Strain context: ATCC 15439. Xue et al. 1998 (PMID:9770448, DOI:10.1073/pnas.95.21.12111) and GenBank AF079762.1 explicitly identify Streptomyces venezuelae ATCC 15439 as the sequenced desosamine (des) subcluster host for BGC0000898:1 (split onto replacement structure CHEBI:32540). Preserve NCBITaxon:54571 and existing SOURCE_ASSERTION/CLUSTER_UNSTATED grades; tautomeric and deposit-partition boundaries remain tracked in #1012. See issue #1010. Taxon identity and evidence grade are unchanged; this is not a species-wide experiment. MIBiG source row BGC0000898:1; SHA256 1c3876fb6e15ecdbd0e4724f6af87e536ae9e4acdba5b97d7cf5381641555eae. Curator: antigravity; date: 2026-10-22.

Occurrences 0

None cited.

Biosynthetic gene clusters 1

AccessionHostLocus evidenceGenome
mibig:BGC0000898 Streptomyces venezuelae
NCBITaxon:54571 		CLUSTER_UNSTATED genbank:AF079762.1

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 DesIV dTDP-glucose 4,6-dehydratase
UniProtKB:Q9ZGH3		 RHEA:17221 CHEBI:15700 → CHEBI:16128 DOI:10.1074/jbc.M310134200
2 DesI dTDP-4-keto-6-deoxy-D-glucose 4-aminotransferase
UniProtKB:Q9ZGH0		 CHEBI:16128 → CHEBI:68523 DOI:10.1021/bi700751d
3 DesII dTDP-4-amino-4,6-dideoxy-alpha-D-glucose ammonia-lyase
UniProtKB:Q9ZGH1		 RHEA:39647 CHEBI:68523 → CHEBI:27645 DOI:10.1021/ja903354k
4 DesV dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucose transaminase
UniProtKB:Q9ZGH4		 RHEA:39907 CHEBI:27645 → CHEBI:10502 DOI:10.1110/ps.062711007
5 DesVI dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
UniProtKB:Q9ZGH6		 RHEA:31759 CHEBI:10502 → CHEBI:27948 DOI:10.1021/bi020245j

Step 1: DesIV (AAC68681.1, AF079762.1:5661..6674, EC 4.2.1.46) catalyzes NAD+-dependent 4,6-dehydration of dTDP-alpha-D-glucose (CHEBI:15700) to dTDP-4-dehydro-6-deoxy-alpha-D-glucose (CHEBI:16128) in the Streptomyces venezuelae ATCC 15439 dTDP-D-desosamine pathway. RHEA:17221 represents the same reaction using the anionic species CHEBI:57477 and CHEBI:57649.

Step 2: DesI (AAC68684.1, AF079762.1:8651..9898, EC 2.6.1.33) catalyzes the PLP-dependent C-4 transamination of dTDP-4-dehydro-6-deoxy-alpha-D-glucose (CHEBI:16128) to dTDP-4-amino-4,6-dideoxy-alpha-D-glucose (CHEBI:68523).

Step 3: DesII (AAC68683.1, AF079762.1:7140..8597, EC 4.3.1.30) is a radical SAM [4Fe-4S] ammonia-lyase that catalyzes the redox-neutral C-4 deamination of dTDP-4-amino-4,6-dideoxy-alpha-D-glucose (CHEBI:68523) to dTDP-3-dehydro-4,6-dideoxy-alpha-D-glucose (CHEBI:27645) and NH4+. RHEA:39647 represents the same reaction using the anionic species CHEBI:68501 and CHEBI:76280.

Step 4: DesV (AAC68680.1, AF079762.1:4502..5641, EC 2.6.1.106) catalyzes the PLP-dependent C-3 transamination of dTDP-3-dehydro-4,6-dideoxy-alpha-D-glucose (CHEBI:27645) with L-glutamate to form dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucose (CHEBI:10502). RHEA:39907 represents the same reaction using the anionic species CHEBI:76280 and CHEBI:63262.

Step 5: DesVI (AAC68678.1, AF079762.1:2811..3524, EC 2.1.1.234) catalyzes the SAM-dependent C-3 N,N-dimethylation of dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucose (CHEBI:10502) to form dTDP-alpha-D-desosamine (CHEBI:27948). This enzymatic pathway terminates at the nucleotide-activated donor dTDP-alpha-D-desosamine (CHEBI:27948; anionic Rhea species CHEBI:63260) rather than asserting an enzymatic release of free desosamine (CHEBI:32540).

Mechanism & Biosynthesis Overview

PRODUCERS & OCCURRENCE 1 producer (0 causal) 0 cited occurrences BIOSYNTHETIC LOCUS 1 gene cluster 5 curated pathway steps NATURAL PRODUCT desosamine CHEBI:32540 Carbohydrates TARGETS & BIOACTIVITY 0 molecular targets 0 bioactivities · 1 graph

Causal graph — biosynthesis 11 nodes, 10 edges

Streptomyces venezuelae ATCC 15439 DesIV/DesI/DesII/DesV/DesVI enzymatic pathway from dTDP-alpha-D-glucose (CHEBI:15700) to the nucleotide-activated donor dTDP-alpha-D-desosamine (CHEBI:27948). Free desosamine (CHEBI:32540) is the deoxysugar moiety transferred from dTDP-alpha-D-desosamine onto macrolactone aglycones by DesVII/DesVIII.

SubjectPredicateObjectNotesEvidence
dTDP-alpha-D-glucose is dehydrated by DesIV dTDP-glucose 4,6-dehydratase DesIV catalyzes RHEA:17221 4,6-dehydration of dTDP-alpha-D-glucose (grounded here to neutral CHEBI:15700 rather than anionic CHEBI:57477).
DOI:10.1074/jbc.M310134200
DOI:10.1073/pnas.95.21.12111
https://www.uniprot.org/uniprotkb/Q9ZGH3
https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
RHEA:17221
  • reference
    DOI:10.1074/jbc.M310134200
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    The desIV gene from Streptomyces venezuelae was cloned, overexpressed in Escherichia coli, and purified to homogeneity
    notes
    Allard et al. (PMID:14570895) cloned, overexpressed, purified, and determined the 1.7-A X-ray crystal structure of Streptomyces venezuelae DesIV (dTDP-glucose 4,6-dehydratase) in complex with dTDP and dTDP-glucose (PDB 1R66 and 1R6D).
  • reference
    DOI:10.1073/pnas.95.21.12111
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    Dedicated to the biosynthesis of dTDP-D-desosamine, an essential deoxysugar component in the macrolide antibiotics methymycin, neomethymycin, narbomycin, and pikromycin
    notes
    Xue et al. (PMID:9770448) sequenced the Streptomyces venezuelae ATCC 15439 pik/des cluster (AF079762.1 / BGC0000898) and identified the desI-desVIII locus for dTDP-D-desosamine biosynthesis and transfer.
  • reference
    https://www.uniprot.org/uniprotkb/Q9ZGH3
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    Active UniProtKB:Q9ZGH3 (337 aa, gene desIV) in Streptomyces venezuelae cross-references EMBL AF079762 protein AAC68681.1, PDB 1R66 and 1R6D, EC 4.2.1.46, and RHEA:17221.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    GenBank AF079762.1 (MIBiG BGC0000898) annotates desIV at CDS 5661..6674 with protein_id AAC68681.1 as dTDP-glucose 4,6-dehydratase.
  • reference
    RHEA:17221
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    RHEA:17221 grounds EC 4.2.1.46 conversion of dTDP-alpha-D-glucose(2-) (CHEBI:57477) to dTDP-4-dehydro-6-deoxy-alpha-D-glucose(2-) (CHEBI:57649) and H2O; this record uses the corresponding neutral ChEBI identifiers CHEBI:15700 and CHEBI:16128.
DesIV dTDP-glucose 4,6-dehydratase forms dTDP-4-dehydro-6-deoxy-alpha-D-glucose DesIV forms dTDP-4-dehydro-6-deoxy-alpha-D-glucose (grounded here to neutral CHEBI:16128 rather than anionic CHEBI:57649).
DOI:10.1074/jbc.M310134200
DOI:10.1073/pnas.95.21.12111
https://www.uniprot.org/uniprotkb/Q9ZGH3
https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
RHEA:17221
  • reference
    DOI:10.1074/jbc.M310134200
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    The desIV gene from Streptomyces venezuelae was cloned, overexpressed in Escherichia coli, and purified to homogeneity
    notes
    Allard et al. (PMID:14570895) cloned, overexpressed, purified, and determined the 1.7-A X-ray crystal structure of Streptomyces venezuelae DesIV (dTDP-glucose 4,6-dehydratase) in complex with dTDP and dTDP-glucose (PDB 1R66 and 1R6D).
  • reference
    DOI:10.1073/pnas.95.21.12111
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    Dedicated to the biosynthesis of dTDP-D-desosamine, an essential deoxysugar component in the macrolide antibiotics methymycin, neomethymycin, narbomycin, and pikromycin
    notes
    Xue et al. (PMID:9770448) sequenced the Streptomyces venezuelae ATCC 15439 pik/des cluster (AF079762.1 / BGC0000898) and identified the desI-desVIII locus for dTDP-D-desosamine biosynthesis and transfer.
  • reference
    https://www.uniprot.org/uniprotkb/Q9ZGH3
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    Active UniProtKB:Q9ZGH3 (337 aa, gene desIV) in Streptomyces venezuelae cross-references EMBL AF079762 protein AAC68681.1, PDB 1R66 and 1R6D, EC 4.2.1.46, and RHEA:17221.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    GenBank AF079762.1 (MIBiG BGC0000898) annotates desIV at CDS 5661..6674 with protein_id AAC68681.1 as dTDP-glucose 4,6-dehydratase.
  • reference
    RHEA:17221
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    RHEA:17221 grounds EC 4.2.1.46 conversion of dTDP-alpha-D-glucose(2-) (CHEBI:57477) to dTDP-4-dehydro-6-deoxy-alpha-D-glucose(2-) (CHEBI:57649) and H2O; this record uses the corresponding neutral ChEBI identifiers CHEBI:15700 and CHEBI:16128.
dTDP-4-dehydro-6-deoxy-alpha-D-glucose is transaminated by DesI dTDP-4-keto-6-deoxy-D-glucose 4-aminotransferase DesI catalyzes PLP-dependent C-4 transamination of dTDP-4-dehydro-6-deoxy-alpha-D-glucose (CHEBI:16128).
DOI:10.1021/bi700751d
DOI:10.1073/pnas.95.21.12111
https://www.uniprot.org/uniprotkb/Q9ZGH0
https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
  • reference
    DOI:10.1021/bi700751d
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    DesI, the third enzyme in the pathway, catalyzes the conversion of dTDP-4-keto-6-deoxyglucose to dTDP-4-amino-4,6-dideoxyglucose
    notes
    Burgie, Thoden, and Holden (PMID:17630700) characterized Streptomyces venezuelae DesI and solved its X-ray crystal structures in the internal aldimine form and in complex with its product dTDP-4-amino-4,6-dideoxyglucose (PDB 2PO3 and 2PZJ).
  • reference
    DOI:10.1073/pnas.95.21.12111
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    Dedicated to the biosynthesis of dTDP-D-desosamine, an essential deoxysugar component in the macrolide antibiotics methymycin, neomethymycin, narbomycin, and pikromycin
    notes
    Xue et al. (PMID:9770448) identified desI in the Streptomyces venezuelae ATCC 15439 des deoxysugar locus (AF079762.1 / BGC0000898) and showed by gene disruption that desI is essential for desosamine biosynthesis.
  • reference
    https://www.uniprot.org/uniprotkb/Q9ZGH0
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    Active UniProtKB:Q9ZGH0 (415 aa, gene desI) in Streptomyces venezuelae cross-references EMBL AF079762 protein AAC68684.1, PDB 2PO3 and 2PZJ, and EC 2.6.1.33.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    GenBank AF079762.1 (MIBiG BGC0000898) annotates desI at CDS 8651..9898 with protein_id AAC68684.1.
DesI dTDP-4-keto-6-deoxy-D-glucose 4-aminotransferase forms dTDP-4-amino-4,6-dideoxy-alpha-D-glucose DesI forms dTDP-4-amino-4,6-dideoxy-alpha-D-glucose (grounded here to neutral CHEBI:68523).
DOI:10.1021/bi700751d
DOI:10.1073/pnas.95.21.12111
https://www.uniprot.org/uniprotkb/Q9ZGH0
https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
  • reference
    DOI:10.1021/bi700751d
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    DesI, the third enzyme in the pathway, catalyzes the conversion of dTDP-4-keto-6-deoxyglucose to dTDP-4-amino-4,6-dideoxyglucose
    notes
    Burgie, Thoden, and Holden (PMID:17630700) characterized Streptomyces venezuelae DesI and solved its X-ray crystal structures in the internal aldimine form and in complex with its product dTDP-4-amino-4,6-dideoxyglucose (PDB 2PO3 and 2PZJ).
  • reference
    DOI:10.1073/pnas.95.21.12111
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    Dedicated to the biosynthesis of dTDP-D-desosamine, an essential deoxysugar component in the macrolide antibiotics methymycin, neomethymycin, narbomycin, and pikromycin
    notes
    Xue et al. (PMID:9770448) identified desI in the Streptomyces venezuelae ATCC 15439 des deoxysugar locus (AF079762.1 / BGC0000898) and showed by gene disruption that desI is essential for desosamine biosynthesis.
  • reference
    https://www.uniprot.org/uniprotkb/Q9ZGH0
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    Active UniProtKB:Q9ZGH0 (415 aa, gene desI) in Streptomyces venezuelae cross-references EMBL AF079762 protein AAC68684.1, PDB 2PO3 and 2PZJ, and EC 2.6.1.33.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    GenBank AF079762.1 (MIBiG BGC0000898) annotates desI at CDS 8651..9898 with protein_id AAC68684.1.
dTDP-4-amino-4,6-dideoxy-alpha-D-glucose is deaminated by DesII dTDP-4-amino-4,6-dideoxy-alpha-D-glucose ammonia-lyase DesII catalyzes RHEA:39647 radical SAM redox-neutral C-4 deamination of dTDP-4-amino-4,6-dideoxy-alpha-D-glucose (grounded here to neutral CHEBI:68523 rather than anionic CHEBI:68501).
DOI:10.1021/ja903354k
DOI:10.1021/ja909451a
https://www.uniprot.org/uniprotkb/Q9ZGH1
https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
RHEA:39647
  • reference
    DOI:10.1021/ja903354k
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    DesII is a radical SAM enzyme found in the biosynthetic pathway of D-desosamine which catalyzes the deamination of TDP-4-amino-4,6-dideoxy-D-glucose to form TDP-3-keto-4,6-dideoxy-D-glucose
    notes
    Ruszczycky et al. (PMID:19746907) demonstrated purified Streptomyces venezuelae DesII radical SAM ammonia-lyase activity converting TDP-4-amino-4,6-dideoxy-D-glucose to TDP-3-keto-4,6-dideoxy-D-glucose via a C3 alpha-hydroxyalkyl radical intermediate.
  • reference
    DOI:10.1021/ja909451a
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    DesII is a radical SAM enzyme responsible for the redox-neutral deamination of TDP-4-amino-4,6-dideoxy-D-glucose to yield TDP-3-keto-4,6-dideoxy-D-glucose in the biosynthesis of TDP-D-desosamine
    notes
    Ruszczycky et al. (PMID:20121093) established the reaction stoichiometry and radical deamination mechanism of Streptomyces venezuelae DesII.
  • reference
    https://www.uniprot.org/uniprotkb/Q9ZGH1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    Reviewed Swiss-Prot UniProtKB:Q9ZGH1 (485 aa, gene desII) in Streptomyces venezuelae cross-references EMBL AF079762 protein AAC68683.1, EC 4.3.1.30, and RHEA:39647.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    GenBank AF079762.1 (MIBiG BGC0000898) annotates desII at CDS 7140..8597 with protein_id AAC68683.1.
  • reference
    RHEA:39647
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    RHEA:39647 grounds EC 4.3.1.30 deamination of dTDP-4-amino-4,6-dideoxy-alpha-D-glucose(1-) (CHEBI:68501) to dTDP-3-dehydro-4,6-dideoxy-alpha-D-glucose(2-) (CHEBI:76280) and NH4+; this record uses the corresponding neutral ChEBI identifiers CHEBI:68523 and CHEBI:27645.
DesII dTDP-4-amino-4,6-dideoxy-alpha-D-glucose ammonia-lyase forms dTDP-3-dehydro-4,6-dideoxy-alpha-D-glucose DesII forms dTDP-3-dehydro-4,6-dideoxy-alpha-D-glucose (grounded here to neutral CHEBI:27645 rather than anionic CHEBI:76280).
DOI:10.1021/ja903354k
DOI:10.1021/ja909451a
https://www.uniprot.org/uniprotkb/Q9ZGH1
https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
RHEA:39647
  • reference
    DOI:10.1021/ja903354k
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    DesII is a radical SAM enzyme found in the biosynthetic pathway of D-desosamine which catalyzes the deamination of TDP-4-amino-4,6-dideoxy-D-glucose to form TDP-3-keto-4,6-dideoxy-D-glucose
    notes
    Ruszczycky et al. (PMID:19746907) demonstrated purified Streptomyces venezuelae DesII radical SAM ammonia-lyase activity converting TDP-4-amino-4,6-dideoxy-D-glucose to TDP-3-keto-4,6-dideoxy-D-glucose via a C3 alpha-hydroxyalkyl radical intermediate.
  • reference
    DOI:10.1021/ja909451a
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    DesII is a radical SAM enzyme responsible for the redox-neutral deamination of TDP-4-amino-4,6-dideoxy-D-glucose to yield TDP-3-keto-4,6-dideoxy-D-glucose in the biosynthesis of TDP-D-desosamine
    notes
    Ruszczycky et al. (PMID:20121093) established the reaction stoichiometry and radical deamination mechanism of Streptomyces venezuelae DesII.
  • reference
    https://www.uniprot.org/uniprotkb/Q9ZGH1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    Reviewed Swiss-Prot UniProtKB:Q9ZGH1 (485 aa, gene desII) in Streptomyces venezuelae cross-references EMBL AF079762 protein AAC68683.1, EC 4.3.1.30, and RHEA:39647.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    GenBank AF079762.1 (MIBiG BGC0000898) annotates desII at CDS 7140..8597 with protein_id AAC68683.1.
  • reference
    RHEA:39647
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    RHEA:39647 grounds EC 4.3.1.30 deamination of dTDP-4-amino-4,6-dideoxy-alpha-D-glucose(1-) (CHEBI:68501) to dTDP-3-dehydro-4,6-dideoxy-alpha-D-glucose(2-) (CHEBI:76280) and NH4+; this record uses the corresponding neutral ChEBI identifiers CHEBI:68523 and CHEBI:27645.
dTDP-3-dehydro-4,6-dideoxy-alpha-D-glucose is transaminated by DesV dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucose transaminase DesV catalyzes RHEA:39907 PLP-dependent C-3 transamination of dTDP-3-dehydro-4,6-dideoxy-alpha-D-glucose (grounded here to neutral CHEBI:27645 rather than anionic CHEBI:76280).
DOI:10.1110/ps.062711007
https://www.uniprot.org/uniprotkb/Q9ZGH4
https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
RHEA:39907
  • reference
    DOI:10.1110/ps.062711007
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    DesV catalyzes the transfer of the amino group from glutamate to the C-3 position of the sugar component of dTDP-3-keto-4,6-dideoxy-D-glucose to yield dTDP-3-amino-3,4,6-trideoxy-D-glucose
    notes
    Burgie and Holden (PMID:17456741) characterized Streptomyces venezuelae DesV and determined its X-ray crystal structures in complex with PLP and the ketimine intermediate (PDB 2OGA and 2OGE).
  • reference
    https://www.uniprot.org/uniprotkb/Q9ZGH4
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    Reviewed Swiss-Prot UniProtKB:Q9ZGH4 (379 aa, gene desV) in Streptomyces venezuelae cross-references EMBL AF079762 protein AAC68680.1, PDB 2OGA and 2OGE, EC 2.6.1.106, and RHEA:39907.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    GenBank AF079762.1 (MIBiG BGC0000898) annotates desV at CDS 4502..5641 with protein_id AAC68680.1.
  • reference
    RHEA:39907
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    RHEA:39907 grounds EC 2.6.1.106 transamination of dTDP-3-dehydro-4,6-dideoxy-alpha-D-glucose(2-) (CHEBI:76280) to dTDP-3-azaniumyl-3,4,6-trideoxy-alpha-D-glucose(1-) (CHEBI:63262); this record uses the corresponding neutral ChEBI identifiers CHEBI:27645 and CHEBI:10502.
DesV dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucose transaminase forms dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucose DesV forms dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucose (grounded here to neutral CHEBI:10502 rather than zwitterionic/anionic CHEBI:63262).
DOI:10.1110/ps.062711007
https://www.uniprot.org/uniprotkb/Q9ZGH4
https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
RHEA:39907
  • reference
    DOI:10.1110/ps.062711007
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    DesV catalyzes the transfer of the amino group from glutamate to the C-3 position of the sugar component of dTDP-3-keto-4,6-dideoxy-D-glucose to yield dTDP-3-amino-3,4,6-trideoxy-D-glucose
    notes
    Burgie and Holden (PMID:17456741) characterized Streptomyces venezuelae DesV and determined its X-ray crystal structures in complex with PLP and the ketimine intermediate (PDB 2OGA and 2OGE).
  • reference
    https://www.uniprot.org/uniprotkb/Q9ZGH4
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    Reviewed Swiss-Prot UniProtKB:Q9ZGH4 (379 aa, gene desV) in Streptomyces venezuelae cross-references EMBL AF079762 protein AAC68680.1, PDB 2OGA and 2OGE, EC 2.6.1.106, and RHEA:39907.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    GenBank AF079762.1 (MIBiG BGC0000898) annotates desV at CDS 4502..5641 with protein_id AAC68680.1.
  • reference
    RHEA:39907
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    RHEA:39907 grounds EC 2.6.1.106 transamination of dTDP-3-dehydro-4,6-dideoxy-alpha-D-glucose(2-) (CHEBI:76280) to dTDP-3-azaniumyl-3,4,6-trideoxy-alpha-D-glucose(1-) (CHEBI:63262); this record uses the corresponding neutral ChEBI identifiers CHEBI:27645 and CHEBI:10502.
dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucose is N,N-dimethylated by DesVI dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose N,N-dimethyltransferase DesVI catalyzes RHEA:31759 SAM-dependent C-3 N,N-dimethylation of dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucose (grounded here to neutral CHEBI:10502 rather than CHEBI:63262).
DOI:10.1021/bi020245j
DOI:10.1021/bi800063j
https://www.uniprot.org/uniprotkb/Q9ZGH6
https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
RHEA:31759
  • reference
    DOI:10.1021/bi020245j
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    DesVI was confirmed to be an N,N-dimethyltransferase which converts TDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose (6) to TDP-D-desosamine (7), the final step in the biosynthesis of TDP-D-desosamine
    notes
    Chang et al. (PMID:12119032) heterologously expressed and purified Streptomyces venezuelae DesVI and demonstrated SAM-dependent N,N-dimethylation of TDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose to TDP-D-desosamine in vitro.
  • reference
    DOI:10.1021/bi800063j
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    DesVI is an S-adenosylmethionine (SAM)-dependent N,N-dimethyltransferase involved in the biosynthesis of dTDP-D-desosamine in Streptomyces venezuelae
    notes
    Burgie, Holden, and Thoden (PMID:18327916) determined the 1.45-A X-ray crystal structure of Streptomyces venezuelae DesVI in complex with SAM (PDB 3BXO).
  • reference
    https://www.uniprot.org/uniprotkb/Q9ZGH6
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    Reviewed Swiss-Prot UniProtKB:Q9ZGH6 (237 aa, gene desVI) in Streptomyces venezuelae cross-references EMBL AF079762 protein AAC68678.1, PDB 3BXO, EC 2.1.1.234, and RHEA:31759.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    GenBank AF079762.1 (MIBiG BGC0000898) annotates desVI at CDS 2811..3524 with protein_id AAC68678.1.
  • reference
    RHEA:31759
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    RHEA:31759 grounds EC 2.1.1.234 N,N-dimethylation of dTDP-3-azaniumyl-3,4,6-trideoxy-alpha-D-glucose(1-) (CHEBI:63262) to dTDP-alpha-D-desosamine(1-) (CHEBI:63260); this record uses the corresponding neutral ChEBI identifiers CHEBI:10502 and CHEBI:27948.
DesVI dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose N,N-dimethyltransferase forms dTDP-alpha-D-desosamine DesVI forms the terminal nucleotide-activated donor dTDP-alpha-D-desosamine (grounded here to neutral CHEBI:27948 rather than anionic CHEBI:63260).
DOI:10.1021/bi020245j
DOI:10.1021/bi800063j
https://www.uniprot.org/uniprotkb/Q9ZGH6
https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
RHEA:31759
  • reference
    DOI:10.1021/bi020245j
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    DesVI was confirmed to be an N,N-dimethyltransferase which converts TDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose (6) to TDP-D-desosamine (7), the final step in the biosynthesis of TDP-D-desosamine
    notes
    Chang et al. (PMID:12119032) heterologously expressed and purified Streptomyces venezuelae DesVI and demonstrated SAM-dependent N,N-dimethylation of TDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose to TDP-D-desosamine in vitro.
  • reference
    DOI:10.1021/bi800063j
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    DesVI is an S-adenosylmethionine (SAM)-dependent N,N-dimethyltransferase involved in the biosynthesis of dTDP-D-desosamine in Streptomyces venezuelae
    notes
    Burgie, Holden, and Thoden (PMID:18327916) determined the 1.45-A X-ray crystal structure of Streptomyces venezuelae DesVI in complex with SAM (PDB 3BXO).
  • reference
    https://www.uniprot.org/uniprotkb/Q9ZGH6
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    Reviewed Swiss-Prot UniProtKB:Q9ZGH6 (237 aa, gene desVI) in Streptomyces venezuelae cross-references EMBL AF079762 protein AAC68678.1, PDB 3BXO, EC 2.1.1.234, and RHEA:31759.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/AF079762.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    GenBank AF079762.1 (MIBiG BGC0000898) annotates desVI at CDS 2811..3524 with protein_id AAC68678.1.
  • reference
    RHEA:31759
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-20
    notes
    RHEA:31759 grounds EC 2.1.1.234 N,N-dimethylation of dTDP-3-azaniumyl-3,4,6-trideoxy-alpha-D-glucose(1-) (CHEBI:63262) to dTDP-alpha-D-desosamine(1-) (CHEBI:63260); this record uses the corresponding neutral ChEBI identifiers CHEBI:10502 and CHEBI:27948.

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

Explore across X-Mech

AntibioticMech (desosamine) ↗ MediaIngredientMech (CHEBI:32540) ↗ TaxonMech: Streptomyces venezuelae (NCBITaxon:54571) ↗ PathwayMech (mibig:BGC0000898) ↗

Provenance

Source conceptSourceVersion
BGC0000898MIBIG5
CHEBI:32540CHEBI3-star

This page is generated from data/natural_products/carbohydrates/desosamine-2.yaml, which is generated from the committed inventories. Neither is edited by hand.