1HIY

Binding of nucleotides to NDP kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Binding of Nucleotides to Nucleoside Diphosphate Kinase: A Calorimetric Study.

Cervoni, L.Lascu, I.Xu, Y.Gonin, P.Morr, M.Merouani, M.Janin, J.Giartosio, A.

(2001) Biochemistry 40: 4583


  • PubMed Abstract: 
  • The source of affinity for substrates of human nucleoside diphosphate (NDP) kinases is particularly important in that its knowledge could be used to design more effective antiviral nucleoside drugs (e.g., AZT). We carried out a microcalorimetric stud ...

    The source of affinity for substrates of human nucleoside diphosphate (NDP) kinases is particularly important in that its knowledge could be used to design more effective antiviral nucleoside drugs (e.g., AZT). We carried out a microcalorimetric study of the binding of enzymes from two organisms to various nucleotides. Isothermal titration calorimetry has been used to characterize the binding in terms of Delta G degrees, Delta H degrees and Delta S degrees. Thermodynamic parameters of the interaction of ADP with the hexameric NDP kinase from Dictyostelium discoideum and with the tetrameric enzyme from Myxococcus xanthus, at 20 degrees C, were similar and, in both cases, binding was enthalpy-driven. The interactions of ADP, 2'deoxyADP, GDP, and IDP with the eukaryotic enzyme differed in enthalpic and entropic terms, whereas the Delta G degrees values obtained were similar due to enthalpy--entropy compensation. The binding of the enzyme to nonphysiological nucleotides, such as AMP--PNP, 3'deoxyADP, and 3'-deoxy-3'-amino-ADP, appears to differ in several respects. Crystallography of the protein bound to 3'-deoxy-3'-amino-ADP showed that the drug was in a distorted position, and was unable to interact correctly with active site side chains. The interaction of pyrimidine nucleoside diphosphates with the hexameric enzyme is characterized by a lower affinity than that with purine nucleotides. Titration showed the stoichiometry of the interaction to be abnormal, with 9--12 binding sites/hexamer. The presence of supplementary binding sites might have physiological implications.


    Organizational Affiliation

    Istituto Pasteur Fondazione Cenci Bolognetti, Università di Roma La Sapienza, 5 P. le Aldo Moro, 00185 Roma, Italy.




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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3AN
Query on 3AN

Download SDF File 
Download CCD File 
A, B, C
3'-DEOXY 3'-AMINO ADENOSINE-5'-DIPHOSPHATE
C10 H16 N6 O9 P2
VKODIDNZKBYXJO-QYYRPYCUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3ANKd: 830000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.220 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.620α = 90.00
b = 71.620β = 90.00
c = 153.800γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORrefinement
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-05-31
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance