5Z5Q

Nukacin ISK-1 in active state


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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

  • DOI: 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 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.


    Organizational Affiliation

    Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Laboratory of Microbial Technology, Kyushu University, Fukuoka, 812-8581, Japan. sonomoto@agr.kyushu-u.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lantibiotic nukacinA27Staphylococcus warneriMutation(s): 0 
Gene Names: nukA
UniProt
Find proteins for Q9KWM4 (Staphylococcus warneri)
Explore Q9KWM4 
Go to UniProtKB:  Q9KWM4
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DBU
Query on DBU
APEPTIDE LINKINGC4 H7 N O2THR
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 
  • OLDERADO: 5Z5Q Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release