Crystal structure of the enolpyruvyl transferase NikO from Streptomyces tendae

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

Starting Model: experimental
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Structural and functional characterization of NikO, an enolpyruvyl transferase essential in nikkomycin biosynthesis.

Oberdorfer, G.Binter, A.Ginj, C.Macheroux, P.Gruber, K.

(2012) J Biol Chem 287: 31427-31436

  • DOI: https://doi.org/10.1074/jbc.M112.352096
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Nikkomycins are peptide-nucleoside compounds with fungicidal, acaricidal, and insecticidal properties because of their strong inhibition of chitin synthase. Thus, they are potential antibiotics especially for the treatment of immunosuppressed patients, for those undergoing chemotherapy, or after organ transplants. Although their chemical structure has been known for more than 30 years, only little is known about their complex biosynthesis. The genes encoding for proteins involved in the biosynthesis of the nucleoside moiety of nikkomycins are co-transcribed in the same operon, comprising the genes nikIJKLMNO. The gene product NikO was shown to belong to the family of enolpyruvyl transferases and to catalyze the transfer of an enolpyruvyl moiety from phosphoenolpyruvate to the 3'-hydroxyl group of UMP. Here, we report activity and inhibition studies of the wild-type enzyme and the variants C130A and D342A. The x-ray crystal structure revealed differences between NikO and its homologs. Furthermore, our studies led to conclusions concerning substrate binding and preference as well as to conclusions about inhibition/alkylation by the antibiotic fosfomycin.

  • Organizational Affiliation

    Institute of Molecular Biosciences, University of Graz, A-8010 Graz, Austria.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NikO protein
A, B
479Streptomyces tendaeMutation(s): 4 
Gene Names: nikO
Find proteins for Q712I1 (Streptomyces tendae)
Explore Q712I1 
Go to UniProtKB:  Q712I1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ712I1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.21α = 90
b = 120.05β = 90
c = 153.21γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2013-01-09
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description