5ZCN

Solution NMR structure of a new lasso peptide brevunsin

• PDB DOI: https://doi.org/10.2210/pdb5ZCN/pdb
• BMRB: 36167

• Classification: UNKNOWN FUNCTION
• Organism(s): Brevundimonas diminuta
• Expression System: Novosphingobium subterraneum
• Mutation(s): No 


• Deposited: 2018-02-19 Released: 2018-10-17 
• Deposition Author(s): Hemmi, H., Kodani, S., Miyake, Y., Kaweewan, I., Nakagawa, H.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 300 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Literature

Heterologous production of a new lasso peptide brevunsin in Sphingomonas subterranea

Kodani, S., Hemmi, H., Miyake, Y., Kaweewan, I., Nakagawa, H.

(2018) J Ind Microbiol Biotechnol 45: 983-992

• PubMed: 30191430 
• DOI: https://doi.org/10.1007/s10295-018-2077-6
• Primary Citation of Related Structures:  
  5ZCN


• PubMed Abstract: 
  

  A shuttle vector pHSG396Sp was constructed to perform gene expression using Sphingomonas subterranea as a host. A new lasso peptide biosynthetic gene cluster, derived from Brevundimonas diminuta, was amplified by PCR and integrated to afford a expression vector pHSG396Sp-12697L. The new lasso peptide brevunsin was successfully produced by S. subterranea, harboring the expression vector, with a high production yield (10.2 mg from 1 L culture). The chemical structure of brevunsin was established by NMR and MS/MS experiments. Based on the information obtained from the NOE experiment, the three-dimensional structure of brevunsin was determined, which indicated that brevunsin possessed a typical lasso structure. This expression vector system provides a new heterologous production method for unexplored lasso peptides that are encoded by bacterial genomes.

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Organizational Affiliation: 

College of Agriculture, Academic Institute, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan. [e-mail].

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: 2.25 kDa 
• Atom Count: 155 
• Modelled Residue Count: 21 
• Deposited Residue Count: 21 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
brevunsin	A	21	Brevundimonas diminuta	Mutation(s): 0
UniProt
Find proteins for A0A381AKI5 (Brevundimonas diminuta) Explore A0A381AKI5  Go to UniProtKB:  A0A381AKI5

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 300 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Hemmi, H., Kodani, S., Miyake, Y., Kaweewan, I., Nakagawa, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	25350964

Revision History  

• Version 1.0: 2018-10-17
  Type: Initial release
  
• Version 1.1: 2018-10-24
  Changes: Data collection, Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Other