Genomic loci for this biosynthetic pathway

Cluster Type From To
The following clusters are from record BGC0001108.1:
Cluster 1Polyketide175778

BGC0001108, pederin biosynthetic gene cluster from symbiont bacterium. Locus 1. Full MIBiG entry.

Chemical compounds

Compound: pederin
PubChem ID: 5381287
SMILES string: Copy to clipboard
Molecular formula: C25H45NO9
Average molecular mass: 503.633 Da
Molecular activity: Cytotoxic, Inhibitor, Other
Molecular target: inhibition of protein biosynthesis caused by binding to the ribosome. This mechanism causes a ribotoxic stress response and ultimately apoptosis.

Class-specific details

Biosynthetic class(es):
Polyketide subclass:
Other (linear)
Polyketide synthase subclass:
Trans-AT type I
Starter unit:
Thioesterase type:
Type I
Release / cyclization type:

Gene cluster description

pederin (BGC0001108). Gene Cluster 1. Biosynthetic class = Polyketide. GenBank AY328023, positions 6372-58844. Click on genes for more information.


biosynthetic genes
transport-related genes
regulatory genes
other genes

Domain annotation

Homologous known gene clusters

General MIBiG information on this cluster

Complete gene cluster sequence?complete
Evidence for cluster-compound connection:Enzymatic assays, Sequence-based prediction
Comments:Pederin is most likely not released by the TE domain but by PedG.
Contact for this cluster:Eric J. N. Helfrich (Institute of Microbiology, Eidgenoessische Technische Hochschule (ETH) Zurich, Piel lab)

Literature references

1. Piel J. (2002) A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles. Proc Natl Acad Sci U S A 99(22):14002-7. doi:
2. Poplau P et al. (2013) An enzymatic domain for the formation of cyclic ethers in complex polyketides. Angew Chem Int Ed Engl 52(50):13215-8. doi: 10.1002/anie.201307406.
3. Zimmermann K et al. (2009) Pederin-type pathways of uncultivated bacterial symbionts: analysis of o-methyltransferases and generation of a biosynthetic hybrid. J Am Chem Soc 131(8):2780-1. doi: 10.1021/ja808889k.
4. Lee KH et al. (2005) Inhibition of protein synthesis and activation of stress-activated protein kinases by onnamide A and theopederin B, antitumor marine natural products. Cancer Sci 96(6):357-64. doi: 10.1111/j.1349-7006.2005.00055.x.
5. Nishimura S et al. (2005) 13-Deoxytedanolide, a marine sponge-derived antitumor macrolide, binds to the 60S large ribosomal subunit. Bioorg Med Chem 13(2):449-54. doi: 10.1016/j.bmc.2004.10.012.
6. Piel J. (2010) Biosynthesis of polyketides by trans-AT polyketide synthases. Nat Prod Rep 27(7):996-1047. doi: 10.1039/b816430b. Epub 2010 May 12.
7. C. Cardani, C. Fuganti, D. Ghiringhelli, P. Grasselli, M. Pavan, M.D. Valcurone. (1973) The biosynthesis of pederin. Tetrahedron Letters, vol. 14, no. 30, pp. 2815-2818
8. Takeshi Matsumoto, Mitsutoshi Yanagiya, Sawae Maeno, Seiichi Yasuda. (1968) A revised structure of pederin. Tetrahedron Letters, vol. 9, no. 60, pp. 6297-6300
9. C. Cardani, D. Ghiringhelli, A. Quilico, A. Selva. (1967) The structure of pederone a novel substance from (coleoptera staphylinidae).. Tetrahedron Letters, vol. 8, no. 41, pp. 4023-4025
10. M. Jacobs-Lorena, A. Brega, C. Baglioni. (1971) Inhibition of protein synthesis in reticulocytes by antibiotics. Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis, vol. 240, no. 2, pp. 263-272