5Z5Q

Nukacin ISK-1 in active state

• PDB DOI:  https://doi.org/10.2210/pdb5Z5Q/pdb
• BMRB: 36157

• Classification: ANTIBIOTIC
• Organism(s): Staphylococcus warneri
• Mutation(s): No 


• Deposited: 2018-01-19 Released: 2018-11-28 
• Deposition Author(s): Kohda, D., Fujinami, D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

The lantibiotic nukacin ISK-1 exists in an equilibrium between active and inactive lipid-II binding states.

Fujinami, D., Mahin, A.A., Elsayed, K.M., Islam, M.R., Nagao, J.I., Roy, U., Momin, S., Zendo, T., Kohda, D., Sonomoto, K.

(2018) Commun Biol 1: 150-150

• PubMed: 30272026 
• DOI: https://doi.org/10.1038/s42003-018-0150-3
• Primary Citation of Related Structures:  
  5Z5Q, 5Z5R


• PubMed Abstract: 
  

The lantibiotic nukacin ISK-1 exerts antimicrobial activity through binding to lipid II. Here, we perform NMR analyses of the structure of nukacin ISK-1 and the interaction with lipid II. Unexpectedly, nukacin ISK-1 exists in two structural states in aqueous solution, with an interconversion rate on a time scale of seconds. The two structures differ in the relative orientations of the two lanthionine rings, ring A and ring C. Chemical shift perturbation induced by the titration of lipid II reveals that only one state was capable of binding to lipid II. On the molecular surface of the active state, a multiple hydrogen-bonding site formed by amino acid residues in the ring A region is adjacent to a hydrophobic surface formed by residues in the ring C region, and we propose that these sites interact with the pyrophosphate moiety and the isoprene chain of the lipid II molecule, respectively.

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Organizational Affiliation: 

Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Laboratory of Microbial Technology, Kyushu University, Fukuoka, 812-8581, 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: 2.97 kDa 
• Atom Count: 205 
• Modelled Residue Count: 27 
• Deposited Residue Count: 27 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lantibiotic nukacin	A	27	Staphylococcus warneri	Mutation(s): 0  Gene Names: nukA
UniProt
Find proteins for Q9KWM4 (Staphylococcus warneri) Explore Q9KWM4  Go to UniProtKB:  Q9KWM4

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DBU	A	PEPTIDE LINKING	C4 H7 N O2		THR

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-28 
Deposition Author(s): Kohda, D., Fujinami, D.

Revision History  

• Version 1.0: 2018-11-28
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Data collection, Database references, Other