2N5C | pdb_00002n5c

Solution NMR structure of the lasso peptide chaxapeptin

• PDB DOI: https://doi.org/10.2210/pdb2N5C/pdb
• BMRB: 25704

• Classification: CELL INVASION
• Organism(s): Streptomyces leeuwenhoekii
• Mutation(s): No 


• Deposited: 2015-07-14 Released: 2015-10-07 
• Deposition Author(s): Elsayed, S.S., Trusch, F., Deng, H., Raab, A., Prokes, I., Busarakam, K., Asenjo, J.A., Andrews, B.A., van West, P., Bull, A.T., Goodfellow, M., Yi, Y., Ebel, R., Jaspars, M., Rateb, M.E.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 15 
• Selection Criteria: structures with acceptable covalent geometry 

Literature

Chaxapeptin, a Lasso Peptide from Extremotolerant Streptomyces leeuwenhoekii Strain C58 from the Hyperarid Atacama Desert.

Elsayed, S.S., Trusch, F., Deng, H., Raab, A., Prokes, I., Busarakam, K., Asenjo, J.A., Andrews, B.A., van West, P., Bull, A.T., Goodfellow, M., Yi, Y., Ebel, R., Jaspars, M., Rateb, M.E.

(2015) J Org Chem 80: 10252-10260

• PubMed: 26402731 
• DOI: https://doi.org/10.1021/acs.joc.5b01878
• Primary Citation of Related Structures:  
  2N5C


• PubMed Abstract: 
  

  Lasso peptides are ribosomally synthesized and post-translationally modified peptides (RiPPs) that possess a unique "lariat knot" structural motif. Genome mining-targeted discovery of new natural products from microbes obtained from extreme environments has led to the identification of a gene cluster directing the biosynthesis of a new lasso peptide, designated as chaxapeptin 1, in the genome of Streptomyces leeuwenhoekii strain C58 isolated from the Atacama Desert. Subsequently, 1 was isolated and characterized using high-resolution electrospray ionization mass spectrometry and nuclear magnetic resonance methods. The lasso nature of 1 was confirmed by calculating its nuclear Overhauser effect restraint-based solution structure. Chaxapeptin 1 displayed a significant inhibitory activity in a cell invasion assay with human lung cancer cell line A549.

---

Organizational Affiliation: 

Marine Biodiscovery Centre, University of Aberdeen , Meston Walk, Aberdeen AB24 3UE, Scotland, U.K.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1.63 kDa 
• Atom Count: 115 
• Modelled Residue Count: 15 
• Deposited Residue Count: 15 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
chaxapeptin	A	15	Streptomyces leeuwenhoekii	Mutation(s): 0
UniProt
Find proteins for A0A0F7VRL1 (Streptomyces leeuwenhoekii) Explore A0A0F7VRL1  Go to UniProtKB:  A0A0F7VRL1

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 15 
• Selection Criteria: structures with acceptable covalent geometry 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-07 
Deposition Author(s): Elsayed, S.S., Trusch, F., Deng, H., Raab, A., Prokes, I., Busarakam, K., Asenjo, J.A., Andrews, B.A., van West, P., Bull, A.T., Goodfellow, M., Yi, Y., Ebel, R., Jaspars, M., Rateb, M.E.

Revision History  

• Version 1.0: 2015-10-07
  Type: Initial release
  
• Version 1.1: 2015-10-28
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary