1B99

3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Catalytic mechanism of nucleoside diphosphate kinase investigated using nucleotide analogues, viscosity effects, and X-ray crystallography.

Gonin, P.Xu, Y.Milon, L.Dabernat, S.Morr, M.Kumar, R.Lacombe, M.L.Janin, J.Lascu, I.

(1999) Biochemistry 38: 7265-7272

  • DOI: 10.1021/bi982990v

  • PubMed Abstract: 
  • Nucleoside diphosphate (NDP) kinases display low specificity with respect to the base moiety of the nucleotides and to the 2'-position of the ribose, but the 3'-hydroxyl is found to be important for catalysis. We report in this paper the enzymatic an ...

    Nucleoside diphosphate (NDP) kinases display low specificity with respect to the base moiety of the nucleotides and to the 2'-position of the ribose, but the 3'-hydroxyl is found to be important for catalysis. We report in this paper the enzymatic analysis of a series of derivatives of thymidine diphosphate (TDP) where the 3'-OH group was removed or replaced by fluorine, azido, and amino groups. With Dictyostelium NDP kinase, kcat decreases 15-200-fold from 1100 s-1 with TDP, and (kcat/Km)NDP decreases from 12 x 10(6) to 10(3) to 5 x 10(4) M-1 s-1, depending on the substrate. The poorest substrates are 3'-deoxyTDP and 3'-azido-3'-deoxyTDP, while the best modified substrates are 2',3'-dehydro-3'-deoxyTDP and 3'-fluoro-3'-deoxyTDP. In a similar way, 3'-fluoro-2',3'-dideoxyUDP was found to be a better substrate than 2',3'-dideoxyUDP, but a much poorer substrate than 2'-deoxyUDP. (kcat/Km)NDP is sensitive to the viscosity of the solution with TDP as the substrate but not with the modified substrates. To understand the poor catalytic efficiency of the modified nucleotides at a structural level, we determined the crystal structure of Dictyostelium NDP kinase complexed to 3'-fluoro-2',3'-dideoxyUDP at 2.7 A resolution. Significant differences are noted as compared to the TDP complex. Substrate-assisted catalysis by the 3'-OH, which is effective in the NDP kinase reaction, cannot occur with the modified substrate. With TDP, the beta-phosphate, which is the leaving group when a gamma-phosphate is transferred to His122, hydrogen bonds to the 3'-hydroxyl group of the sugar; with 3'-fluoro-2',3'-dideoxyUDP, the beta-phosphate hydrogen bonds to Asn119 and moves away from the attacking Ndelta of the catalytic His122. Since all anti-AIDS nucleoside drugs are modified at the 3'-position, these results are relevant to the role of NDP kinase in their cellular metabolism.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

    University of Bordeaux-2, Institut de Biochimie et Génétique Cellulaires, UPR 9026, Centre National de la Recherche Scientifique, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
A, B, C, D, E, F
155Dictyostelium discoideumMutation(s): 0 
Gene 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
FUP
Query on FUP

Download SDF File 
Download CCD File 
A
2',3'-DIDEOXY-3'-FLUORO-URIDIDINE-5'-DIPHOSPHATE
FUDP
C9 H13 F N2 O10 P2
WLQBZMZTRNPUDL-SHYZEUOFSA-N
 Ligand Interaction
POP
Query on POP

Download SDF File 
Download CCD File 
B, C, D, E, F
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.020α = 90.00
b = 105.310β = 117.43
c = 70.350γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling
MOSFLMdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1999-02-22 
  • Released Date: 1999-06-28 
  • Deposition Author(s): Janin, J., Xu, Y.

Revision History 

  • Version 1.0: 1999-06-28
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance