1LWX

AZT DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray analysis of azido-thymidine diphosphate binding to nucleoside diphosphate kinase.

Xu, Y.Sellam, O.Morera, S.Sarfati, S.Biondi, R.Veron, M.Janin, J.

(1997) Proc.Natl.Acad.Sci.USA 94: 7162-7165


  • PubMed Abstract: 
  • To be effective as antiviral agent, AZT (3'-azido-3'-deoxythymidine) must be converted to a triphosphate derivative by cellular kinases. The conversion is inefficient and, to understand why AZT diphosphate is a poor substrate of nucleoside diphosphat ...

    To be effective as antiviral agent, AZT (3'-azido-3'-deoxythymidine) must be converted to a triphosphate derivative by cellular kinases. The conversion is inefficient and, to understand why AZT diphosphate is a poor substrate of nucleoside diphosphate (NDP) kinase, we determined a 2.3-A x-ray structure of a complex with the N119A point mutant of Dictyostelium NDP kinase. It shows that the analog binds at the same site and, except for the sugar ring pucker which is different, binds in the same way as the natural substrate thymidine diphosphate. However, the azido group that replaces the 3'OH of the deoxyribose in AZT displaces a lysine side chain involved in catalysis. Moreover, it is unable to make an internal hydrogen bond to the oxygen bridging the beta- and gamma-phosphate, which plays an important part in phosphate transfer.


    Related Citations: 
    • Adenosine 5'-Diphosphate Binding and the Active Site of Nucleoside Diphosphate Kinase
      Morera, S.,Lascu, I.,Dumas, C.,Lebras, G.,Briozzo, P.,Veron, M.,Janin, J.
      (1994) Biochemistry 33: 459
    • Mechanism of Phosphate Transfer by Nucleoside Diphosphate Kinase: X-Ray Structures of the Phosphohistidine Intermediate of the Enzymes from Drosophila and Dictyostelium
      Morera, S.,Chiadmi, M.,Lebras, G.,Lascu, I.,Janin, J.
      (1995) Biochemistry 34: 11062


    Organizational Affiliation

    Laboratoire d'Enzymologie et de Biochimie Structurales, Unité Propre de Recherche 9063, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEOSIDE DIPHOSPHATE KINASE
A, B, C
155Dictyostelium discoideumGene Names: ndkC-1, ndkC-2 (gip17, ndkB, gip17, ndkB)
EC: 2.7.4.6
Find proteins for P22887 (Dictyostelium discoideum)
Go to UniProtKB:  P22887
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AZD
Query on AZD

Download SDF File 
Download CCD File 
A, B, C
3'-AZIDO-3'-DEOXYTHYMIDINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
QOYVAFWJURKBJG-XLPZGREQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.216 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.590α = 90.00
b = 71.590β = 90.00
c = 152.700γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
MOSFLMdata reduction
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-04-30 
  • Released Date: 1997-08-20 
  • Deposition Author(s): Janin, J., Xu, Y.

Revision History 

  • Version 1.0: 1997-08-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance