5Z5R

Nukacin ISK-1 in inactive 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:  

  • 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 ...

    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

    1Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582 Japan.,3Department of Functional Bioscience, Section of Infection Biology, Fukuoka Dental College, Fukuoka, 814-0175 Japan.,6Present Address: Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000 Bangladesh.,2Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Laboratory of Microbial Technology, Kyushu University, Fukuoka, 812-8581 Japan.,Present Address: Microbiology and Industrial Irradiation Division, Institute of Food and Radiation Biology, Atomic Energy Research Establishment, Ganakbari, Savar 1207, Dhaka, 1349 Bangladesh.,5Present Address: Department of Microbiology, Faculty of Pharmacy, Misr International University, Cairo, 19648 Egypt.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lantibiotic nukacin
A
27Staphylococcus warneriMutation(s): 0 
Gene Names: nukA
Find proteins for Q9KWM4 (Staphylococcus warneri)
Go to UniProtKB:  Q9KWM4
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
DBU
Query on DBU
A
PEPTIDE LINKINGC4 H7 N O2THR
DBB
Query on DBB
A
D-PEPTIDE LINKINGC4 H9 N O2

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DAL
Query on DAL
A
D-PEPTIDE LINKINGC3 H7 N O2

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Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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