1J90

Crystal Structure of Drosophila Deoxyribonucleoside Kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for substrate specificities of cellular deoxyribonucleoside kinases.

Johansson, K.Ramaswamy, S.Ljungcrantz, C.Knecht, W.Piskur, J.Munch-Petersen, B.Eriksson, S.Eklund, H.

(2001) Nat.Struct.Mol.Biol. 8: 616-620

  • DOI: 10.1038/89661
  • Primary Citation of Related Structures:  1JAG, 2OCP

  • PubMed Abstract: 
  • Deoxyribonucleoside kinases phosphorylate deoxyribonucleosides and activate a number of medically important nucleoside analogs. Here we report the structure of the Drosophila deoxyribonucleoside kinase with deoxycytidine bound at the nucleoside bindi ...

    Deoxyribonucleoside kinases phosphorylate deoxyribonucleosides and activate a number of medically important nucleoside analogs. Here we report the structure of the Drosophila deoxyribonucleoside kinase with deoxycytidine bound at the nucleoside binding site and that of the human deoxyguanosine kinase with ATP at the nucleoside substrate binding site. Compared to the human kinase, the Drosophila kinase has a wider substrate cleft, which may be responsible for the broad substrate specificity of this enzyme. The human deoxyguanosine kinase is highly specific for purine substrates; this is apparently due to the presence of Arg 118, which provides favorable hydrogen bonding interactions with the substrate. The two new structures provide an explanation for the substrate specificity of cellular deoxyribonucleoside kinases.


    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, Biomedical Center, S-751 24 Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxyribonucleoside kinase
A, B
230Drosophila melanogasterGene Names: dnk
EC: 2.7.1.145
Find proteins for Q9XZT6 (Drosophila melanogaster)
Go to UniProtKB:  Q9XZT6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCZ
Query on DCZ

Download SDF File 
Download CCD File 
A, B
2'-DEOXYCYTIDINE
C9 H13 N3 O4
CKTSBUTUHBMZGZ-SHYZEUOFSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.238 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 119.456α = 90.00
b = 60.749β = 90.00
c = 67.269γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SOLVEphasing
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance