3WX8

Purification, characterization and structure of nucleoside diphosphate kinase from Drosophila S2 cells


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

wwPDB Validation 3D Report Full Report



Literature

Purification, characterization and structure of nucleoside diphosphate kinase from Drosophila melanogaster

Qian, L.Liu, X.

(2014) Protein Expr Purif 103: 48-55

  • DOI: 10.1016/j.pep.2014.08.014
  • Primary Citation of Related Structures:  
    3WX8

  • PubMed Abstract: 
  • Nucleoside diphosphate kinase (NDPK) is a ubiquitous enzyme found in all organisms and cell types, which catalyzes the transfer of the phosphoryl group from a nucleoside triphosphate to a nucleoside diphosphate. The gene encoding for NDPK from Drosop ...

    Nucleoside diphosphate kinase (NDPK) is a ubiquitous enzyme found in all organisms and cell types, which catalyzes the transfer of the phosphoryl group from a nucleoside triphosphate to a nucleoside diphosphate. The gene encoding for NDPK from Drosophila melanogaster was amplified from the genomic DNA. The recombinant NDPK (rNDPK) was overexpressed in Escherichia coli and purified to homogeneity by Ni-NTA agarose affinity chromatography, HiTrap SP HP cation exchange chromatography and HiLoad 16/60 Superdex 200 gel filtration chromatography. The gel filtration chromatography and analytical ultracentrifugation showed that rNDPK was a trimer in solution. The binding affinity of NDPs with rNDPK, measured by isothermal titration calorimetry, indicated that the purines nucleotides show higher binding affinity compared with pyrimidines. The rNDPK had a definite nuclease activity in vitro, which could cleave supercoiled plasmid DNA, but had no effect on dsDNA and ssDNA. Furthermore, the structure for NDPK was determined by using the sitting drop vapor diffusion method. In the final model, the asymmetric unit is made of three molecules, each of which consists of a four-stranded anti-parallel β-sheets and seven α-helices. Sequence alignment and structure comparison illustrated that the simulated nucleotide-binding active site are conserved.


    Organizational Affiliation

    State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China. Electronic address: liu2008@nankai.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoside diphosphate kinaseA, B, C153Drosophila melanogasterMutation(s): 0 
Gene Names: awdK-pnCG2210
EC: 2.7.4.6
Find proteins for P08879 (Drosophila melanogaster)
Explore P08879 
Go to UniProtKB:  P08879
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.243α = 90
b = 114.243β = 90
c = 94.162γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-07-25 
  • Released Date: 2015-06-10 
  • Deposition Author(s): Qian, L.

Revision History 

  • Version 1.0: 2015-06-10
    Type: Initial release