9KAR | pdb_00009kar

Solution NMR structure of a new lasso peptide streptacidin

• PDB DOI: https://doi.org/10.2210/pdb9KAR/pdb

• Classification: ANTIBIOTIC
• Organism(s): Streptacidiphilus jiangxiensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-29 Released: 2025-04-16 
• Deposition Author(s): Huang, J.W., Cao, C.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Literature

Genome mining and heterologous expression reveal streptacidin, a new lasso peptide from Streptacidiphilus jiangxiensis.

Huang, J., Cheng, B., Cao, C., Liu, W.

(2025) Org Biomol Chem 23: 1723-1730

• PubMed: 39807060 
• DOI: https://doi.org/10.1039/d4ob01998a
• Primary Citation Related Structures: 
  9KAR


• PubMed Abstract: 
  

  A lasso peptide biosynthetic gene cluster (BGC) was identified through genome mining in the species Streptacidiphilus jiangxiensis CGMCC 4.1857, which was isolated from acidic rhizosphere soil. The BGC was reconstructed in Escherichia coli , leading to the heterologous production of a lasso peptide named streptacidin. The solution structure of streptacidin was determined based on the distance constraints derived from the NOESY spectrum, establishing the first lasso peptide utilizing methionine as a steric lock for the unique spatial configuration and the remarkable stability against heat (up to 95 °C) and proteolytic degradation by carboxypeptidase Y and chymotrypsin. Under experimental conditions, streptacidin showed weak effectiveness against vancomycin sensitive Enterococcus faecalis ATCC 29212 and Pseudomonas aeruginosa ATCC 902. These findings further the understanding of this distinctive class of compounds.

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Organizational Affiliation: 
• State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 1.81 kDa 
• Atom Count: 129 
• Modeled Residue Count: 15 
• Deposited Residue Count: 15 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-GLY-TRP-GLY-THR-VAL-PRO-ASP-TRP-PHE-PHE-ASN-MET-ASN-TRP	A	15	Streptacidiphilus jiangxiensis	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Huang, J.W., Cao, C.Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22407135
National Natural Science Foundation of China (NSFC)	China	2022YFC2303100

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release