1J90

Crystal Structure of Drosophila Deoxyribonucleoside Kinase

• PDB DOI: https://doi.org/10.2210/pdb1J90/pdb

• Classification: TRANSFERASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-05-23 Released: 2001-11-28 
• Deposition Author(s): Johansson, K., Ramaswamy, S., Ljungkrantz, C., Knecht, W., Piskur, J., Munch-Petersen, B., Eriksson, S., Eklund, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 0.258 
• R-Value Work: 0.238 
• R-Value Observed: 0.260 

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 Biol 8: 616-620

• PubMed: 11427893 
• DOI: https://doi.org/10.1038/89661
• Primary Citation of Related Structures:  
  1J90, 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54.46 kDa 
• Atom Count: 3,404 
• Modelled Residue Count: 386 
• Deposited Residue Count: 460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribonucleoside kinase	A, B	230	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for Q9XZT6 (Drosophila melanogaster) Explore Q9XZT6  Go to UniProtKB:  Q9XZT6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCZ	D [auth A], F [auth B]	2'-DEOXYCYTIDINE C9 H13 N3 O4 CKTSBUTUHBMZGZ-SHYZEUOFSA-N
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 0.258 
• R-Value Work: 0.238 
• R-Value Observed: 0.260 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.456	α = 90
b = 60.749	β = 90
c = 67.269	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-11-28 
Deposition Author(s): Johansson, K., Ramaswamy, S., Ljungkrantz, C., Knecht, W., Piskur, J., Munch-Petersen, B., Eriksson, S., Eklund, H.

Revision History  

• Version 1.0: 2001-11-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations