2VPP

Drosophila melanogaster deoxyribonucleoside kinase successfully activates gemcitabine in transduced cancer cell lines

• PDB DOI: https://doi.org/10.2210/pdb2VPP/pdb

• Classification: TRANSFERASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2008-03-03 Released: 2009-03-24 
• Deposition Author(s): Knecht, W., Mikkelsen, N.E., Clausen, A., Willer, M., Gojkovic, Z., Piskur, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.253 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Starting Model: experimental

Literature

Drosophila Melanogaster Deoxyribonucleoside Kinase Activates Gemcitabine.

Knecht, W., Mikkelsen, N.E., Clausen, A., Willer, M., Eklund, H., Gojkovic, Z., Piskur, J.

(2009) Biochem Biophys Res Commun 382: 430

• PubMed: 19285960 
• DOI: https://doi.org/10.1016/j.bbrc.2009.03.041
• Primary Citation of Related Structures:  
  2VPP


• PubMed Abstract: 
  

  Drosophila melanogaster multisubstrate deoxyribonucleoside kinase (Dm-dNK) can additionally sensitize human cancer cell lines towards the anti-cancer drug gemcitabine. We show that this property is based on the Dm-dNK ability to efficiently phosphorylate gemcitabine. The 2.2A resolution structure of Dm-dNK in complex with gemcitabine shows that the residues Tyr70 and Arg105 play a crucial role in the firm positioning of gemcitabine by extra interactions made by the fluoride atoms. This explains why gemcitabine is a good substrate for Dm-dNK.

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Organizational Affiliation: 

BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark.

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 PQS (software)

Macromolecule Content

• Total Structure Weight: 54.53 kDa 
• Atom Count: 3,394 
• Modelled Residue Count: 371 
• Deposited Residue Count: 460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEOXYNUCLEOSIDE KINASE	A, B	230	Drosophila melanogaster	Mutation(s): 0  EC: 2.7.1.145
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
GEO	C [auth A], E [auth B]	GEMCITABINE C9 H11 F2 N3 O4 SDUQYLNIPVEERB-QPPQHZFASA-N
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
GEO	PDBBind:  2VPP	IC50: 760 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.253 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.106	α = 90
b = 62.298	β = 90
c = 68.078	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Knecht, W., Mikkelsen, N.E., Clausen, A., Willer, M., Gojkovic, Z., Piskur, J.

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description