2ZI9

C4S-E247A dCK variant of dCK in complex with cladribine+ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.332 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Elucidation of different binding modes of purine nucleosides to human deoxycytidine kinase

Sabini, E.Hazra, S.Konrad, M.Lavie, A.

(2008) J Med Chem 51: 4219-4225

  • DOI: 10.1021/jm800134t
  • Primary Citation of Related Structures:  
    2ZI9, 2ZI7, 2ZIA

  • PubMed Abstract: 
  • Purine nucleoside analogues of medicinal importance, such as cladribine, require phosphorylation by deoxycytidine kinase (dCK) for pharmacological activity. Structural studies of ternary complexes of human dCK show that the enzyme conformation adjust ...

    Purine nucleoside analogues of medicinal importance, such as cladribine, require phosphorylation by deoxycytidine kinase (dCK) for pharmacological activity. Structural studies of ternary complexes of human dCK show that the enzyme conformation adjusts to the different hydrogen-bonding properties between dA and dG and to the presence of substituent at the 2-position present in dG and cladribine. Specifically, the carbonyl group in dG elicits a previously unseen conformational adjustment of the active site residues Arg104 and Asp133. In addition, dG and cladribine adopt the anti conformation, in contrast to the syn conformation observed with dA. Kinetic analysis reveals that cladribine is phosphorylated at the highest efficiency with UTP as donor. We attribute this to the ability of cladribine to combine advantageous properties from dA (favorable hydrogen-bonding pattern) and dG (propensity to bind to the enzyme in its anti conformation), suggesting that dA analogues with a substituent at the 2-position are likely to be better activated by human dCK.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S. Ashland (M/C 669), Chicago, Illinois 60607, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxycytidine kinaseAB279Homo sapiensMutation(s): 5 
Gene Names: DCK
EC: 2.7.1.74 (PDB Primary Data), 2.7.1.76 (UniProt), 2.7.1.113 (UniProt)
Find proteins for P27707 (Homo sapiens)
Explore P27707 
Go to UniProtKB:  P27707
NIH Common Fund Data Resources
PHAROS  P27707
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CL9
Query on CL9

Download CCD File 
A, B
2-chloro-2'-deoxyadenosine
C10 H12 Cl N5 O3
PTOAARAWEBMLNO-KVQBGUIXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.332 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.239 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.39α = 90
b = 132.71β = 90
c = 157.47γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SERGUIdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2008-02-13 
  • Released Date: 2008-07-08 
  • Deposition Author(s): Sabini, E., Lavie, A.

Revision History 

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance