4CAW | pdb_00004caw

Crystal structure of Aspergillus fumigatus N-myristoyl transferase in complex with myristoyl CoA and a pyrazole sulphonamide ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.299 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.240 (Depositor) 
  • R-Value Observed: 
    0.244 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

N-Myristoyltransferase is a Cell Wall Target in Aspergillus Fumigatus.

Fang, W.Robinson, D.A.Raimi, O.G.Blair, D.E.Harrison, J.R.Lockhart, D.E.A.Torrie, L.S.Ruda, G.F.Wyatt, P.G.Gilbert, I.H.Van Aalten, D.M.F.

(2015) ACS Chem Biol 10: 1425

  • DOI: https://doi.org/10.1021/cb5008647
  • Primary Citation Related Structures: 
    4CAV, 4CAW, 4CAX

  • PubMed Abstract: 

    Treatment of filamentous fungal infections relies on a limited repertoire of antifungal agents. Compounds possessing novel modes of action are urgently required. N-myristoylation is a ubiquitous modification of eukaryotic proteins. The enzyme N-myristoyltransferase (NMT) has been considered a potential therapeutic target in protozoa and yeasts. Here, we show that the filamentous fungal pathogen Aspergillus fumigatus possesses an active NMT enzyme that is essential for survival. Surprisingly, partial repression of the gene revealed downstream effects of N-myristoylation on cell wall morphology. Screening a library of inhibitors led to the discovery of a pyrazole sulphonamide compound that inhibits the enzyme and is fungicidal under partially repressive nmt conditions. Together with a crystallographic complex showing the inhibitor binding in the peptide substrate pocket, we provide evidence of NMT being a potential drug target in A. fumigatus.


  • Organizational Affiliation
    • †Division of Molecular Microbiology, ‡Division of Biological Chemistry and Drug Discovery, §MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 48.96 kDa 
  • Atom Count: 3,362 
  • Modeled Residue Count: 390 
  • Deposited Residue Count: 411 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE411Aspergillus fumigatusMutation(s): 0 
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

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MYA

Query on MYA



Download:Ideal Coordinates CCD File
C [auth A]TETRADECANOYL-COA
C35 H62 N7 O17 P3 S
DUAFKXOFBZQTQE-QSGBVPJFSA-N
P3U

Query on P3U



Download:Ideal Coordinates CCD File
B [auth A]2,6-DICHLORO-4-(2-PIPERAZIN-1-YLPYRIDIN-4-YL)-N-(1,5-DIMETHYL,3-ISOBUTYL-1H-PYRAZOL-4-YL)BENZENESULFONAMIDE
C24 H30 Cl2 N6 O2 S
WKTSLVQYGBHNRV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.299 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.240 (Depositor) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.873α = 90
b = 57.83β = 90
c = 147.514γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other