6POR

Antimicrobial lasso peptide ubonodin

• PDB DOI: https://doi.org/10.2210/pdb6POR/pdb
• BMRB: 30625

• Classification: ANTIBIOTIC
• Organism(s): Burkholderia ubonensis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2019-07-05 Released: 2019-12-04 
• Deposition Author(s): Link, A.J., Cheung-Lee, W.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Discovery of Ubonodin, an Antimicrobial Lasso Peptide Active against Members of the Burkholderia cepacia Complex.

Cheung-Lee, W.L., Parry, M.E., Zong, C., Cartagena, A.J., Darst, S.A., Connell, N.D., Russo, R., Link, A.J.

(2020) Chembiochem 21: 1335-1340

• PubMed: 31765515 
• DOI: https://doi.org/10.1002/cbic.201900707
• Primary Citation of Related Structures:  
  6POR


• PubMed Abstract: 
  

  We report the heterologous expression, structure, and antimicrobial activity of a lasso peptide, ubonodin, encoded in the genome of Burkholderia ubonensis. The topology of ubonodin is unprecedented amongst lasso peptides, with 18 of its 28 amino acids found in the mechanically bonded loop segment. Ubonodin inhibits RNA polymerase in vitro and has potent antimicrobial activity against several pathogenic members of the Burkholderia genus, most notably B. cepacia and B. multivorans, causative agents of lung infections in cystic fibrosis patients.

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Organizational Affiliation: 

Department of Chemical and Biological Engineering, Princeton University, 207 Hoyt Laboratory, Princeton, NJ, 08544, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 3.22 kDa 
• Atom Count: 226 
• Modelled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubonodin	A	28	Burkholderia ubonensis	Mutation(s): 0  Gene Names: WJ58_02830

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-12-04 
Deposition Author(s): Link, A.J., Cheung-Lee, W.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM107036

Revision History  

• Version 1.0: 2019-12-04
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2020-05-20
  Changes: Database references
• Version 1.4: 2023-06-14
  Changes: Database references, Other