Aspergillus fumigatus Af293 NDK

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.141 

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Characterization of crystal structure and key residues of Aspergillus fumigatus nucleoside diphosphate kinase.

Hu, Y.Jia, X.Lu, Z.Han, L.

(2019) Biochem Biophys Res Commun 511: 148-153

  • DOI: https://doi.org/10.1016/j.bbrc.2019.01.126
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Aspergillus fumigatus is a major pathogen of invasive pulmonary aspergillosis with high mortality rate. The nucleoside diphosphate kinase of A. fumigatus, AfNDK (also called SwoH) is essential for its viability, however, its structural characteristic was unknown. In this study, we solved the crystal structure of AfNDK and found that it exists predominantly in form of tetramer in solution. Oligomeric form rather than dimeric form was essential for its kinase activity. The Arg30 and the C terminal amino acids were crucial for dimer-dimer interaction and the viability of A. fumigatus. Mutation V83F might make the secondary structure α5 helix protrude outward so that the whole protein structure became unstable at higher temperature, which might subsequently result to the inviability of A. fumigatus under 44 °C. In conclusion, the crystal structure of AfNDK was for the first time analyzed and the stability of the tetrameric form with dimer-dimer interaction were crucial for its function in A. fumigatus.

  • Organizational Affiliation

    Center for Disease Control and Prevention of Chinese PLA, Beijing, 100071, China; Academy of Military Medical Sciences, 27(#) Taiping Road, Haidian District, Beijing, 100101, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase161Aspergillus fumigatus Af293Mutation(s): 0 
Find proteins for Q7Z8P9 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293))
Explore Q7Z8P9 
Go to UniProtKB:  Q7Z8P9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z8P9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.141 
  • Space Group: P 3 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.756α = 90
b = 70.756β = 90
c = 53.095γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2019-03-13 
  • Deposition Author(s): Hu, Y., Han, L.

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description