4QBJ

Crystal structure of N-myristoyl transferase from Aspergillus fumigatus complexed with a synthetic inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structure of N-myristoyltransferase from Aspergillus fumigatus

Shimada, T.Suzuki, M.Katakura, S.

(2015) Acta Crystallogr D Biol Crystallogr 71: 754-761

  • DOI: https://doi.org/10.1107/S1399004715000401
  • Primary Citation of Related Structures:  
    4QBJ

  • PubMed Abstract: 

    N-Myristoyltransferase (NMT) is an enzyme which translocates the 14-carbon saturated fatty acid myristate from myristoyl-CoA to the N-terminal glycine of substrate peptides. This myristoylation process is involved in protein modification in various eukaryotes, including animals and fungi. Furthermore, this enzyme has been shown to be essential to the growth of various species, such as Saccharomyces cerevisiae, which indicates that NMT is an attractive target for the development of a novel antifungal drug. In this study, the crystal structure of a ternary complex of NMT from Aspergillus fumigatus with S-(2-oxo)pentadecyl-CoA, a myristoyl-CoA analogue cofactor, and a synthetic inhibitor is reported at a resolution of 2.1 Å. The results advance the understanding of the specificity of NMT inhibitors and provide valuable information for structure-based drug design.


  • Organizational Affiliation

    Drug Discovery and Biomedical Technology Unit, Daiichi Sankyo RD Novare Co. Ltd, 1-16-13 Kita-kasai, Edogawa-ku, Tokyo 134-8630, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycylpeptide N-tetradecanoyltransferase396Aspergillus fumigatus Af293Mutation(s): 0 
Gene Names: nmt1
EC: 2.3.1.97
UniProt
Find proteins for Q9UVX3 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293))
Explore Q9UVX3 
Go to UniProtKB:  Q9UVX3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UVX3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.792α = 90
b = 77.074β = 90
c = 113.237γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references
  • Version 1.2: 2015-04-22
    Changes: Database references
  • Version 1.3: 2016-12-21
    Changes: Structure summary
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description